From 2963adbca9a51103cce0642bb71a97683096a70f Mon Sep 17 00:00:00 2001 From: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com> Date: Mon, 22 Jul 2024 10:15:10 +0200 Subject: [PATCH] Backport PR #837 to 1.0.x (#842) * Concatenate_h5mu: fix writing multi-dimensional annotation frames. (#837) * Concatenate_h5mu: fix writing multidomensional annotation frames. * Undo some changes * Update test * Add PR number * Trigger CI * Update CHANGELOG * deploy: 57add3ff137ac44d67bc7456cb9146bc6dc633cc * Update CHANGELOG --------- Co-authored-by: DriesSchaumont --- CHANGELOG.md | 9 +++ src/dataflow/concatenate_h5mu/script.py | 10 ++- src/dataflow/concatenate_h5mu/test.py | 62 +++++++++++++++++-- target/docker/annotate/popv/.config.vsh.yaml | 6 +- target/docker/annotate/popv/popv | 12 ++-- target/docker/cluster/leiden/.config.vsh.yaml | 6 +- target/docker/cluster/leiden/leiden | 12 ++-- .../compress_h5mu/.config.vsh.yaml | 6 +- .../compression/compress_h5mu/compress_h5mu | 12 ++-- .../compression/tar_extract/.config.vsh.yaml | 6 +- .../compression/tar_extract/tar_extract | 12 ++-- .../from_10xh5_to_h5mu/.config.vsh.yaml | 6 +- .../from_10xh5_to_h5mu/from_10xh5_to_h5mu | 12 ++-- .../from_10xmtx_to_h5mu/.config.vsh.yaml | 6 +- .../from_10xmtx_to_h5mu/from_10xmtx_to_h5mu | 12 ++-- 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+-- .../metadata/join_uns_to_obs/nextflow.config | 2 +- .../move_obsm_to_obs/.config.vsh.yaml | 6 +- .../metadata/move_obsm_to_obs/main.nf | 8 +-- .../metadata/move_obsm_to_obs/nextflow.config | 2 +- .../nextflow/neighbors/bbknn/.config.vsh.yaml | 6 +- target/nextflow/neighbors/bbknn/main.nf | 8 +-- .../nextflow/neighbors/bbknn/nextflow.config | 2 +- .../neighbors/find_neighbors/.config.vsh.yaml | 6 +- .../nextflow/neighbors/find_neighbors/main.nf | 8 +-- .../neighbors/find_neighbors/nextflow.config | 2 +- .../filter_10xh5/.config.vsh.yaml | 6 +- .../process_10xh5/filter_10xh5/main.nf | 8 +-- .../filter_10xh5/nextflow.config | 2 +- .../qc/calculate_qc_metrics/.config.vsh.yaml | 6 +- .../nextflow/qc/calculate_qc_metrics/main.nf | 8 +-- .../qc/calculate_qc_metrics/nextflow.config | 2 +- target/nextflow/qc/fastqc/.config.vsh.yaml | 6 +- target/nextflow/qc/fastqc/main.nf | 8 +-- target/nextflow/qc/fastqc/nextflow.config | 2 +- target/nextflow/qc/multiqc/.config.vsh.yaml | 6 +- target/nextflow/qc/multiqc/main.nf | 8 +-- target/nextflow/qc/multiqc/nextflow.config | 2 +- .../query/cellxgene_census/.config.vsh.yaml | 6 +- .../nextflow/query/cellxgene_census/main.nf | 8 +-- .../query/cellxgene_census/nextflow.config | 2 +- .../build_bdrhap_reference/.config.vsh.yaml | 6 +- .../reference/build_bdrhap_reference/main.nf | 8 +-- .../build_bdrhap_reference/nextflow.config | 2 +- .../.config.vsh.yaml | 6 +- .../build_cellranger_reference/main.nf | 8 +-- .../nextflow.config | 2 +- .../reference/make_reference/.config.vsh.yaml | 6 +- .../nextflow/reference/make_reference/main.nf | 8 +-- .../reference/make_reference/nextflow.config | 2 +- .../nextflow/report/mermaid/.config.vsh.yaml | 6 +- target/nextflow/report/mermaid/main.nf | 8 +-- .../nextflow/report/mermaid/nextflow.config | 2 +- .../transfer/publish/.config.vsh.yaml | 6 +- target/nextflow/transfer/publish/main.nf | 8 +-- .../nextflow/transfer/publish/nextflow.config | 2 +- .../nextflow/transform/clr/.config.vsh.yaml | 6 +- target/nextflow/transform/clr/main.nf | 8 +-- target/nextflow/transform/clr/nextflow.config | 2 +- .../transform/delete_layer/.config.vsh.yaml | 6 +- .../nextflow/transform/delete_layer/main.nf | 8 +-- .../transform/delete_layer/nextflow.config | 2 +- .../nextflow/transform/log1p/.config.vsh.yaml | 6 +- target/nextflow/transform/log1p/main.nf | 8 +-- .../nextflow/transform/log1p/nextflow.config | 2 +- .../transform/move_layer/.config.vsh.yaml | 6 +- target/nextflow/transform/move_layer/main.nf | 8 +-- .../transform/move_layer/nextflow.config | 2 +- .../normalize_total/.config.vsh.yaml | 6 +- .../transform/normalize_total/main.nf | 8 +-- .../transform/normalize_total/nextflow.config | 2 +- .../transform/regress_out/.config.vsh.yaml | 6 +- target/nextflow/transform/regress_out/main.nf | 8 +-- .../transform/regress_out/nextflow.config | 2 +- .../nextflow/transform/scale/.config.vsh.yaml | 6 +- target/nextflow/transform/scale/main.nf | 8 +-- .../nextflow/transform/scale/nextflow.config | 2 +- .../nextflow/velocity/scvelo/.config.vsh.yaml | 6 +- target/nextflow/velocity/scvelo/main.nf | 8 +-- .../nextflow/velocity/scvelo/nextflow.config | 2 +- .../velocity/velocyto/.config.vsh.yaml | 6 +- target/nextflow/velocity/velocyto/main.nf | 8 +-- .../velocity/velocyto/nextflow.config | 2 +- .../gdo/gdo_singlesample/.config.vsh.yaml | 14 ++--- .../workflows/gdo/gdo_singlesample/main.nf | 16 ++--- .../gdo/gdo_singlesample/nextflow.config | 2 +- .../ingestion/bd_rhapsody/.config.vsh.yaml | 14 ++--- .../workflows/ingestion/bd_rhapsody/main.nf | 16 ++--- .../ingestion/bd_rhapsody/nextflow.config | 2 +- .../cellranger_mapping/.config.vsh.yaml | 18 +++--- .../ingestion/cellranger_mapping/main.nf | 20 +++--- .../cellranger_mapping/nextflow.config | 2 +- .../cellranger_multi/.config.vsh.yaml | 14 ++--- .../ingestion/cellranger_multi/main.nf | 16 ++--- .../cellranger_multi/nextflow.config | 2 +- .../.config.vsh.yaml | 22 +++---- .../cellranger_postprocessing/main.nf | 24 +++---- .../cellranger_postprocessing/nextflow.config | 2 +- .../ingestion/conversion/.config.vsh.yaml | 18 +++--- .../workflows/ingestion/conversion/main.nf | 20 +++--- .../ingestion/conversion/nextflow.config | 2 +- .../ingestion/demux/.config.vsh.yaml | 26 ++++---- .../workflows/ingestion/demux/main.nf | 28 ++++----- .../workflows/ingestion/demux/nextflow.config | 2 +- .../ingestion/make_reference/.config.vsh.yaml | 22 +++---- .../ingestion/make_reference/main.nf | 24 +++---- .../ingestion/make_reference/nextflow.config | 2 +- .../integration/bbknn_leiden/.config.vsh.yaml | 22 +++---- .../integration/bbknn_leiden/main.nf | 24 +++---- .../integration/bbknn_leiden/nextflow.config | 2 +- .../harmony_leiden/.config.vsh.yaml | 26 ++++---- .../integration/harmony_leiden/main.nf | 28 ++++----- .../harmony_leiden/nextflow.config | 2 +- .../scanorama_leiden/.config.vsh.yaml | 26 ++++---- .../integration/scanorama_leiden/main.nf | 28 ++++----- .../scanorama_leiden/nextflow.config | 2 +- .../integration/scvi_leiden/.config.vsh.yaml | 26 ++++---- .../workflows/integration/scvi_leiden/main.nf | 28 ++++----- .../integration/scvi_leiden/nextflow.config | 2 +- .../totalvi_leiden/.config.vsh.yaml | 30 ++++----- .../integration/totalvi_leiden/main.nf | 32 +++++----- .../totalvi_leiden/nextflow.config | 2 +- .../dimensionality_reduction/.config.vsh.yaml | 18 +++--- .../dimensionality_reduction/main.nf | 20 +++--- .../dimensionality_reduction/nextflow.config | 2 +- .../process_batches/.config.vsh.yaml | 34 +++++----- .../multiomics/process_batches/main.nf | 36 +++++------ .../process_batches/nextflow.config | 2 +- .../process_samples/.config.vsh.yaml | 42 ++++++------- .../multiomics/process_samples/main.nf | 44 ++++++------- .../process_samples/nextflow.config | 2 +- .../split_modalities/.config.vsh.yaml | 10 +-- .../multiomics/split_modalities/main.nf | 12 ++-- .../split_modalities/nextflow.config | 2 +- .../prot/prot_multisample/.config.vsh.yaml | 14 ++--- .../workflows/prot/prot_multisample/main.nf | 16 ++--- .../prot/prot_multisample/nextflow.config | 2 +- .../prot/prot_singlesample/.config.vsh.yaml | 14 ++--- .../workflows/prot/prot_singlesample/main.nf | 16 ++--- .../prot/prot_singlesample/nextflow.config | 2 +- .../nextflow/workflows/qc/qc/.config.vsh.yaml | 18 +++--- target/nextflow/workflows/qc/qc/main.nf | 20 +++--- .../nextflow/workflows/qc/qc/nextflow.config | 2 +- .../rna/rna_multisample/.config.vsh.yaml | 30 ++++----- .../workflows/rna/rna_multisample/main.nf | 32 +++++----- .../rna/rna_multisample/nextflow.config | 2 +- .../rna/rna_singlesample/.config.vsh.yaml | 26 ++++---- .../workflows/rna/rna_singlesample/main.nf | 28 ++++----- .../rna/rna_singlesample/nextflow.config | 2 +- 573 files changed, 2368 insertions(+), 2251 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1a74de71328..9752b024437 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,12 @@ +# openpipelines 1.0.2 + +## BUG FIXES + +* `dataflow/concatenate_h5mu`: fix writing out multidimensional annotation dataframes (e.g. `.varm`) that had their + data dtype (dtype) changed as a result of adding more observations after concatenation, causing `TypeError`. + One notable example of this happening is when one of the samples does not have a multimodal annotation dataframe + which is present in another sample; causing the values being filled with `NA` (PR #842, backported from PR #837). + # openpipelines 1.0.1 ## BUG FIXES diff --git a/src/dataflow/concatenate_h5mu/script.py b/src/dataflow/concatenate_h5mu/script.py index 4fda2e332c8..cb2a1c288f0 100644 --- a/src/dataflow/concatenate_h5mu/script.py +++ b/src/dataflow/concatenate_h5mu/script.py @@ -220,7 +220,15 @@ def split_conflicts_modalities(n_processes: int, samples: dict[str, anndata.AnnD output_index = getattr(output, matrix_name).index conflicts, concatenated_matrix = concatenate_matrices(n_processes, matrices, output_index) if concatenated_matrix.empty: - concatenated_matrix.index = output_index + concatenated_matrix.index = output_index + + # Even though we did not touch the varm and obsm matrices that were already present, + # the joining of observations might have caused a dtype change in these matrices as well + # so these also need to be casted to a writable dtype... + for multidim_name, multidim_data in getattr(output, f"{matrix_name}m").items(): + new_data = cast_to_writeable_dtype(multidim_data) if isinstance(multidim_data, pd.DataFrame) else multidim_data + getattr(output, f"{matrix_name}m")[multidim_name] = new_data + # Write the conflicts to the output for conflict_name, conflict_data in conflicts.items(): getattr(output, f"{matrix_name}m")[conflict_name] = conflict_data diff --git a/src/dataflow/concatenate_h5mu/test.py b/src/dataflow/concatenate_h5mu/test.py index 8b75a9a8079..784c769367d 100644 --- a/src/dataflow/concatenate_h5mu/test.py +++ b/src/dataflow/concatenate_h5mu/test.py @@ -478,9 +478,14 @@ def test_concat_different_columns_per_modality_and_per_sample(run_component, sam non_shared_features = data_sample1.var_names.difference(data_sample2.var_names) assert concatenated_data.var.loc[non_shared_features, 'mod2:Feat4'].isna().all() -@pytest.mark.parametrize("test_value,expected", [("bar", "bar"), (True, True), (0.1, 0.1), (np.nan, pd.NA)]) +@pytest.mark.parametrize("test_value,test_value_dtype,expected", [("bar", "str", "bar"), + (True, pd.BooleanDtype(), True), + (1, pd.Int16Dtype(), 1), + (0.1, float, 0.1), + (0.1, np.float64, 0.1), + (np.nan, np.float64, pd.NA)]) def test_concat_remove_na(run_component, sample_1_h5mu, sample_2_h5mu, - write_mudata_to_file, random_h5mu_path, test_value, expected, + write_mudata_to_file, random_h5mu_path, test_value, test_value_dtype, expected, change_column_contents): """ Test concatenation of samples where the column from one sample contains NA values @@ -492,7 +497,7 @@ def test_concat_remove_na(run_component, sample_1_h5mu, sample_2_h5mu, """ change_column_contents(sample_1_h5mu, 'var', 'Shared_feat', {'mod1': np.nan, 'mod2': np.nan}) change_column_contents(sample_2_h5mu, 'var', 'Shared_feat', {'mod1': test_value, 'mod2': np.nan}) - + sample_2_h5mu.var['Shared_feat'] = sample_2_h5mu.var['Shared_feat'].astype(test_value_dtype) output_path = random_h5mu_path() run_component([ @@ -547,9 +552,17 @@ def test_concat_invalid_h5_error_includes_path(run_component, tmp_path, err.value.stdout.decode('utf-8')) -@pytest.mark.parametrize("test_value_1,test_value_2,expected", [(1, "1", pd.CategoricalDtype(categories=['1.0', '1']))]) +@pytest.mark.parametrize("test_value_1,value_1_dtype,test_value_2,value_2_dtype,expected", + [(1, float, "1", str, pd.CategoricalDtype(categories=['1.0', '1'])), + (1, np.float64, "1", str, pd.CategoricalDtype(categories=['1.0', '1'])), + (1, pd.Int16Dtype(), 2.0, pd.Int16Dtype(), pd.Int64Dtype()), + (True, bool, False, bool, pd.BooleanDtype()), + (True, pd.BooleanDtype(), False, bool, pd.BooleanDtype()), + ("foo", str, "bar", str, pd.CategoricalDtype(categories=['bar', 'foo'])), + ] + ) def test_concat_dtypes_per_modality(run_component, write_mudata_to_file, change_column_contents, - sample_1_h5mu, sample_2_h5mu, test_value_1, test_value_2, + sample_1_h5mu, sample_2_h5mu, test_value_1, value_1_dtype, test_value_2, value_2_dtype, expected, random_h5mu_path): """ Test joining column with different dtypes to make sure that they are writable. @@ -561,7 +574,10 @@ def test_concat_dtypes_per_modality(run_component, write_mudata_to_file, change_ for the test column in mod2 is still writable. """ change_column_contents(sample_1_h5mu, "var", "test_col", {"mod1": test_value_1, "mod2": test_value_1}) + sample_1_h5mu.var['test_col'] = sample_1_h5mu.var['test_col'].astype(value_1_dtype) change_column_contents(sample_2_h5mu, "var", "test_col", {"mod1": test_value_2, "mod2": test_value_2}) + sample_2_h5mu.var['test_col'] = sample_2_h5mu.var['test_col'].astype(value_2_dtype) + output_file = random_h5mu_path() run_component([ "--input_id", "sample1;sample2", @@ -573,6 +589,40 @@ def test_concat_dtypes_per_modality(run_component, write_mudata_to_file, change_ concatenated_data = md.read(output_file) assert concatenated_data['mod2'].var['test_col'].dtype == expected + +@pytest.mark.parametrize("test_value,value_dtype,expected", + [(1, float, pd.Int64Dtype()), + (1, np.float64, pd.Int64Dtype()), + (1, pd.Int16Dtype(), pd.Int16Dtype()), + (True, bool, pd.BooleanDtype()), + (True, pd.BooleanDtype(), pd.BooleanDtype()), + ("foo", str, pd.CategoricalDtype(categories=['foo'])), + ] + ) +def test_concat_dtypes_per_modality_multidim(run_component, write_mudata_to_file, + sample_1_h5mu, sample_2_h5mu, test_value, value_dtype, + expected, random_h5mu_path): + """ + Test if the result of concatenation is still writable when the input already contain + data in .varm and this data is kept. Because we are joining observations, the dtype of this + data may change and the result might not be writable anymore + """ + + sample_1_h5mu['mod1'].varm['test_df'] = pd.DataFrame(index=sample_1_h5mu['mod1'].var_names) + sample_1_h5mu['mod1'].varm['test_df']['test_col'] = test_value + sample_1_h5mu['mod1'].varm['test_df']['test_col'] = sample_1_h5mu['mod1'].varm['test_df']['test_col'].astype(value_dtype) + + output_file = random_h5mu_path() + run_component([ + "--input_id", "sample1;sample2", + "--input", write_mudata_to_file(sample_1_h5mu), + "--input", write_mudata_to_file(sample_2_h5mu), + "--output", output_file, + "--other_axis_mode", "move" + ]) + concatenated_data = md.read(output_file) + assert concatenated_data['mod1'].varm['test_df']['test_col'].dtype == expected + @pytest.mark.parametrize("test_value_1,test_value_2,expected", [(1, "1", pd.CategoricalDtype(categories=['1.0', '1']))]) def test_concat_dtypes_global(run_component, write_mudata_to_file, change_column_contents, sample_1_h5mu, sample_2_h5mu, test_value_1, test_value_2, @@ -622,6 +672,8 @@ def test_non_overlapping_modalities(run_component, sample_2_h5mu, sample_3_h5mu, "--output", output_path, "--other_axis_mode", "move" ]) + output_data = md.read(output_path) + assert set(output_data.mod.keys()) == {"mod1", "mod2", "mod3"} def test_resolve_annotation_conflict_missing_column(run_component, sample_1_h5mu, diff --git a/target/docker/annotate/popv/.config.vsh.yaml b/target/docker/annotate/popv/.config.vsh.yaml index f7810bb0dac..372292e632b 100644 --- a/target/docker/annotate/popv/.config.vsh.yaml +++ b/target/docker/annotate/popv/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "popv" namespace: "annotate" - version: "1.0.1" + version: "1.0.2" authors: - name: "Matthias Beyens" roles: @@ -352,6 +352,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/annotate/popv" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/annotate/popv/popv" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/annotate/popv/popv b/target/docker/annotate/popv/popv index d112d290b36..2b3b5750098 100755 --- a/target/docker/annotate/popv/popv +++ b/target/docker/annotate/popv/popv @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# popv 1.0.1 +# popv 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "popv 1.0.1" + echo "popv 1.0.2" echo "" echo "Performs popular major vote cell typing on single cell sequence data using" echo "multiple algorithms. Note that this is a one-shot version of PopV." @@ -503,10 +503,10 @@ RUN cd /opt && git clone --depth 1 https://github.com/YosefLab/PopV.git && \ LABEL org.opencontainers.image.authors="Matthias Beyens, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component annotate popv" -LABEL org.opencontainers.image.created="2024-06-18T14:14:56Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:09Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -661,7 +661,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "popv 1.0.1" + echo "popv 1.0.2" exit ;; --input) diff --git a/target/docker/cluster/leiden/.config.vsh.yaml b/target/docker/cluster/leiden/.config.vsh.yaml index b7f84b8baa4..24f2866d56c 100644 --- a/target/docker/cluster/leiden/.config.vsh.yaml +++ b/target/docker/cluster/leiden/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "leiden" namespace: "cluster" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries De Maeyer" roles: @@ -230,6 +230,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/cluster/leiden" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/cluster/leiden/leiden" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/cluster/leiden/leiden b/target/docker/cluster/leiden/leiden index 2ad6597d9ef..5ae48ee85b0 100755 --- a/target/docker/cluster/leiden/leiden +++ b/target/docker/cluster/leiden/leiden @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# leiden 1.0.1 +# leiden 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "leiden 1.0.1" + echo "leiden 1.0.2" echo "" echo "Cluster cells using the [Leiden algorithm] [Traag18] implemented in the [Scanpy" echo "framework] [Wolf18]." @@ -460,10 +460,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries De Maeyer" LABEL org.opencontainers.image.description="Companion container for running component cluster leiden" -LABEL org.opencontainers.image.created="2024-06-18T14:14:57Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:05Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -618,7 +618,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "leiden 1.0.1" + echo "leiden 1.0.2" exit ;; --input) diff --git a/target/docker/compression/compress_h5mu/.config.vsh.yaml b/target/docker/compression/compress_h5mu/.config.vsh.yaml index 3c5eda9b2ab..ae6d88d356a 100644 --- a/target/docker/compression/compress_h5mu/.config.vsh.yaml +++ b/target/docker/compression/compress_h5mu/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "compress_h5mu" namespace: "compression" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -171,6 +171,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/compression/compress_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/compression/compress_h5mu/compress_h5mu" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/compression/compress_h5mu/compress_h5mu b/target/docker/compression/compress_h5mu/compress_h5mu index 8b9af2065d8..31b7c4f0f8d 100755 --- a/target/docker/compression/compress_h5mu/compress_h5mu +++ b/target/docker/compression/compress_h5mu/compress_h5mu @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# compress_h5mu 1.0.1 +# compress_h5mu 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "compress_h5mu 1.0.1" + echo "compress_h5mu 1.0.2" echo "" echo "Compress a MuData file." echo "" @@ -423,10 +423,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component compression compress_h5mu" -LABEL org.opencontainers.image.created="2024-06-18T14:14:58Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:06Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -581,7 +581,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "compress_h5mu 1.0.1" + echo "compress_h5mu 1.0.2" exit ;; --input) diff --git a/target/docker/compression/tar_extract/.config.vsh.yaml b/target/docker/compression/tar_extract/.config.vsh.yaml index 02ac49c0d6f..5b4a2249ba3 100644 --- a/target/docker/compression/tar_extract/.config.vsh.yaml +++ b/target/docker/compression/tar_extract/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "tar_extract" namespace: "compression" - version: "1.0.1" + version: "1.0.2" arguments: - type: "file" name: "--input" @@ -107,6 +107,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/compression/tar_extract" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/compression/tar_extract/tar_extract" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/compression/tar_extract/tar_extract b/target/docker/compression/tar_extract/tar_extract index 5a01748efe8..5ca8aabcd56 100755 --- a/target/docker/compression/tar_extract/tar_extract +++ b/target/docker/compression/tar_extract/tar_extract @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# tar_extract 1.0.1 +# tar_extract 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -170,7 +170,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "tar_extract 1.0.1" + echo "tar_extract 1.0.2" echo "" echo "Extract files from a tar archive" echo "" @@ -421,10 +421,10 @@ ENTRYPOINT [] RUN : LABEL org.opencontainers.image.description="Companion container for running component compression tar_extract" -LABEL org.opencontainers.image.created="2024-06-18T14:14:58Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:06Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -579,7 +579,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "tar_extract 1.0.1" + echo "tar_extract 1.0.2" exit ;; --input) diff --git a/target/docker/convert/from_10xh5_to_h5mu/.config.vsh.yaml b/target/docker/convert/from_10xh5_to_h5mu/.config.vsh.yaml index 67f1e5d109d..dfec7d14e35 100644 --- a/target/docker/convert/from_10xh5_to_h5mu/.config.vsh.yaml +++ b/target/docker/convert/from_10xh5_to_h5mu/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "from_10xh5_to_h5mu" namespace: "convert" - version: "1.0.1" + version: "1.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -277,6 +277,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/from_10xh5_to_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/from_10xh5_to_h5mu/from_10xh5_to_h5mu" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/convert/from_10xh5_to_h5mu/from_10xh5_to_h5mu b/target/docker/convert/from_10xh5_to_h5mu/from_10xh5_to_h5mu index 247560ebdb6..7dbfdd28c3e 100755 --- a/target/docker/convert/from_10xh5_to_h5mu/from_10xh5_to_h5mu +++ b/target/docker/convert/from_10xh5_to_h5mu/from_10xh5_to_h5mu @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# from_10xh5_to_h5mu 1.0.1 +# from_10xh5_to_h5mu 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "from_10xh5_to_h5mu 1.0.1" + echo "from_10xh5_to_h5mu 1.0.2" echo "" echo "Converts a 10x h5 into an h5mu file." echo "" @@ -445,10 +445,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component convert from_10xh5_to_h5mu" -LABEL org.opencontainers.image.created="2024-06-18T14:14:59Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:12Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -603,7 +603,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "from_10xh5_to_h5mu 1.0.1" + echo "from_10xh5_to_h5mu 1.0.2" exit ;; --input) diff --git a/target/docker/convert/from_10xmtx_to_h5mu/.config.vsh.yaml b/target/docker/convert/from_10xmtx_to_h5mu/.config.vsh.yaml index 9eff71af525..ac88440b1b6 100644 --- a/target/docker/convert/from_10xmtx_to_h5mu/.config.vsh.yaml +++ b/target/docker/convert/from_10xmtx_to_h5mu/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "from_10xmtx_to_h5mu" namespace: "convert" - version: "1.0.1" + version: "1.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -171,6 +171,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/from_10xmtx_to_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/from_10xmtx_to_h5mu/from_10xmtx_to_h5mu" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/convert/from_10xmtx_to_h5mu/from_10xmtx_to_h5mu b/target/docker/convert/from_10xmtx_to_h5mu/from_10xmtx_to_h5mu index 0f867f01d91..5b8aa0d27b4 100755 --- a/target/docker/convert/from_10xmtx_to_h5mu/from_10xmtx_to_h5mu +++ b/target/docker/convert/from_10xmtx_to_h5mu/from_10xmtx_to_h5mu @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# from_10xmtx_to_h5mu 1.0.1 +# from_10xmtx_to_h5mu 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "from_10xmtx_to_h5mu 1.0.1" + echo "from_10xmtx_to_h5mu 1.0.2" echo "" echo "Converts a 10x mtx into an h5mu file." echo "" @@ -423,10 +423,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component convert from_10xmtx_to_h5mu" -LABEL org.opencontainers.image.created="2024-06-18T14:14:59Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:12Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -581,7 +581,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "from_10xmtx_to_h5mu 1.0.1" + echo "from_10xmtx_to_h5mu 1.0.2" exit ;; --input) diff --git a/target/docker/convert/from_bd_to_10x_molecular_barcode_tags/.config.vsh.yaml b/target/docker/convert/from_bd_to_10x_molecular_barcode_tags/.config.vsh.yaml index 0088c8c8fff..24555418844 100644 --- a/target/docker/convert/from_bd_to_10x_molecular_barcode_tags/.config.vsh.yaml +++ b/target/docker/convert/from_bd_to_10x_molecular_barcode_tags/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "from_bd_to_10x_molecular_barcode_tags" namespace: "convert" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -162,6 +162,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/from_bd_to_10x_molecular_barcode_tags" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/from_bd_to_10x_molecular_barcode_tags/from_bd_to_10x_molecular_barcode_tags" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/convert/from_bd_to_10x_molecular_barcode_tags/from_bd_to_10x_molecular_barcode_tags b/target/docker/convert/from_bd_to_10x_molecular_barcode_tags/from_bd_to_10x_molecular_barcode_tags index dc84a33457c..b0ad465be79 100755 --- a/target/docker/convert/from_bd_to_10x_molecular_barcode_tags/from_bd_to_10x_molecular_barcode_tags +++ b/target/docker/convert/from_bd_to_10x_molecular_barcode_tags/from_bd_to_10x_molecular_barcode_tags @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# from_bd_to_10x_molecular_barcode_tags 1.0.1 +# from_bd_to_10x_molecular_barcode_tags 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "from_bd_to_10x_molecular_barcode_tags 1.0.1" + echo "from_bd_to_10x_molecular_barcode_tags 1.0.2" echo "" echo "Convert the molecular barcode sequence SAM tag from BD format (MA) to 10X format" echo "(UB)." @@ -424,10 +424,10 @@ RUN apt-get update && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component convert from_bd_to_10x_molecular_barcode_tags" -LABEL org.opencontainers.image.created="2024-06-18T14:15:00Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:11Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -582,7 +582,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "from_bd_to_10x_molecular_barcode_tags 1.0.1" + echo "from_bd_to_10x_molecular_barcode_tags 1.0.2" exit ;; --input) diff --git a/target/docker/convert/from_bdrhap_to_h5mu/.config.vsh.yaml b/target/docker/convert/from_bdrhap_to_h5mu/.config.vsh.yaml index 3b939f54103..0cc5838f8a2 100644 --- a/target/docker/convert/from_bdrhap_to_h5mu/.config.vsh.yaml +++ b/target/docker/convert/from_bdrhap_to_h5mu/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "from_bdrhap_to_h5mu" namespace: "convert" - version: "1.0.1" + version: "1.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -185,6 +185,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/from_bdrhap_to_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/from_bdrhap_to_h5mu/from_bdrhap_to_h5mu" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/convert/from_bdrhap_to_h5mu/from_bdrhap_to_h5mu b/target/docker/convert/from_bdrhap_to_h5mu/from_bdrhap_to_h5mu index 8e63d096650..1ee026ba654 100755 --- a/target/docker/convert/from_bdrhap_to_h5mu/from_bdrhap_to_h5mu +++ b/target/docker/convert/from_bdrhap_to_h5mu/from_bdrhap_to_h5mu @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# from_bdrhap_to_h5mu 1.0.1 +# from_bdrhap_to_h5mu 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "from_bdrhap_to_h5mu 1.0.1" + echo "from_bdrhap_to_h5mu 1.0.2" echo "" echo "Convert the output of a BD Rhapsody WTA pipeline to a MuData h5 file." echo "" @@ -429,10 +429,10 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component convert from_bdrhap_to_h5mu" -LABEL org.opencontainers.image.created="2024-06-18T14:15:01Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:11Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -587,7 +587,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "from_bdrhap_to_h5mu 1.0.1" + echo "from_bdrhap_to_h5mu 1.0.2" exit ;; --id) diff --git a/target/docker/convert/from_cellranger_multi_to_h5mu/.config.vsh.yaml b/target/docker/convert/from_cellranger_multi_to_h5mu/.config.vsh.yaml index ffae96d594e..20834b27058 100644 --- a/target/docker/convert/from_cellranger_multi_to_h5mu/.config.vsh.yaml +++ b/target/docker/convert/from_cellranger_multi_to_h5mu/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "from_cellranger_multi_to_h5mu" namespace: "convert" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -195,6 +195,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/from_cellranger_multi_to_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/from_cellranger_multi_to_h5mu/from_cellranger_multi_to_h5mu" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/convert/from_cellranger_multi_to_h5mu/from_cellranger_multi_to_h5mu b/target/docker/convert/from_cellranger_multi_to_h5mu/from_cellranger_multi_to_h5mu index 135dee31227..066f5149878 100755 --- a/target/docker/convert/from_cellranger_multi_to_h5mu/from_cellranger_multi_to_h5mu +++ b/target/docker/convert/from_cellranger_multi_to_h5mu/from_cellranger_multi_to_h5mu @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# from_cellranger_multi_to_h5mu 1.0.1 +# from_cellranger_multi_to_h5mu 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "from_cellranger_multi_to_h5mu 1.0.1" + echo "from_cellranger_multi_to_h5mu 1.0.2" echo "" echo "Converts the output from cellranger multi to a single .h5mu file." echo "By default, will map the following library type names to modality names:" @@ -442,10 +442,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component convert from_cellranger_multi_to_h5mu" -LABEL org.opencontainers.image.created="2024-06-18T14:15:00Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:10Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -600,7 +600,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "from_cellranger_multi_to_h5mu 1.0.1" + echo "from_cellranger_multi_to_h5mu 1.0.2" exit ;; --input) diff --git a/target/docker/convert/from_h5ad_to_h5mu/.config.vsh.yaml b/target/docker/convert/from_h5ad_to_h5mu/.config.vsh.yaml index 2e987cf5024..bf140830d4b 100644 --- a/target/docker/convert/from_h5ad_to_h5mu/.config.vsh.yaml +++ b/target/docker/convert/from_h5ad_to_h5mu/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "from_h5ad_to_h5mu" namespace: "convert" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries De Maeyer" roles: @@ -189,6 +189,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/from_h5ad_to_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/from_h5ad_to_h5mu/from_h5ad_to_h5mu" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/convert/from_h5ad_to_h5mu/from_h5ad_to_h5mu b/target/docker/convert/from_h5ad_to_h5mu/from_h5ad_to_h5mu index 669cfd8048e..e1106f06435 100755 --- a/target/docker/convert/from_h5ad_to_h5mu/from_h5ad_to_h5mu +++ b/target/docker/convert/from_h5ad_to_h5mu/from_h5ad_to_h5mu @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# from_h5ad_to_h5mu 1.0.1 +# from_h5ad_to_h5mu 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "from_h5ad_to_h5mu 1.0.1" + echo "from_h5ad_to_h5mu 1.0.2" echo "" echo "Converts a single layer h5ad file into a single MuData object" echo "" @@ -427,10 +427,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries De Maeyer" LABEL org.opencontainers.image.description="Companion container for running component convert from_h5ad_to_h5mu" -LABEL org.opencontainers.image.created="2024-06-18T14:15:00Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:11Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -585,7 +585,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "from_h5ad_to_h5mu 1.0.1" + echo "from_h5ad_to_h5mu 1.0.2" exit ;; --input) diff --git a/target/docker/convert/from_h5mu_to_h5ad/.config.vsh.yaml b/target/docker/convert/from_h5mu_to_h5ad/.config.vsh.yaml index 89b15712186..5fc658f2efb 100644 --- a/target/docker/convert/from_h5mu_to_h5ad/.config.vsh.yaml +++ b/target/docker/convert/from_h5mu_to_h5ad/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "from_h5mu_to_h5ad" namespace: "convert" - version: "1.0.1" + version: "1.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -194,6 +194,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/from_h5mu_to_h5ad" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/from_h5mu_to_h5ad/from_h5mu_to_h5ad" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/convert/from_h5mu_to_h5ad/from_h5mu_to_h5ad b/target/docker/convert/from_h5mu_to_h5ad/from_h5mu_to_h5ad index d5215cfc34c..0e4cab21edb 100755 --- a/target/docker/convert/from_h5mu_to_h5ad/from_h5mu_to_h5ad +++ b/target/docker/convert/from_h5mu_to_h5ad/from_h5mu_to_h5ad @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# from_h5mu_to_h5ad 1.0.1 +# from_h5mu_to_h5ad 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "from_h5mu_to_h5ad 1.0.1" + echo "from_h5mu_to_h5ad 1.0.2" echo "" echo "Converts a h5mu file into a h5ad file." echo "" @@ -428,10 +428,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component convert from_h5mu_to_h5ad" -LABEL org.opencontainers.image.created="2024-06-18T14:14:59Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:10Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -586,7 +586,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "from_h5mu_to_h5ad 1.0.1" + echo "from_h5mu_to_h5ad 1.0.2" exit ;; --input) diff --git a/target/docker/convert/from_h5mu_to_seurat/.config.vsh.yaml b/target/docker/convert/from_h5mu_to_seurat/.config.vsh.yaml index e494b78899c..1a17b62c52e 100644 --- a/target/docker/convert/from_h5mu_to_seurat/.config.vsh.yaml +++ b/target/docker/convert/from_h5mu_to_seurat/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "from_h5mu_to_seurat" namespace: "convert" - version: "1.0.1" + version: "1.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -186,6 +186,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/from_h5mu_to_seurat" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/from_h5mu_to_seurat/from_h5mu_to_seurat" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/convert/from_h5mu_to_seurat/from_h5mu_to_seurat b/target/docker/convert/from_h5mu_to_seurat/from_h5mu_to_seurat index 48441019674..1bb28c495f6 100755 --- a/target/docker/convert/from_h5mu_to_seurat/from_h5mu_to_seurat +++ b/target/docker/convert/from_h5mu_to_seurat/from_h5mu_to_seurat @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# from_h5mu_to_seurat 1.0.1 +# from_h5mu_to_seurat 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "from_h5mu_to_seurat 1.0.1" + echo "from_h5mu_to_seurat 1.0.2" echo "" echo "Converts an h5mu file into a Seurat file." echo "" @@ -442,10 +442,10 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component convert from_h5mu_to_seurat" -LABEL org.opencontainers.image.created="2024-06-18T14:15:00Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:10Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -600,7 +600,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "from_h5mu_to_seurat 1.0.1" + echo "from_h5mu_to_seurat 1.0.2" exit ;; --input) diff --git a/target/docker/convert/velocyto_to_h5mu/.config.vsh.yaml b/target/docker/convert/velocyto_to_h5mu/.config.vsh.yaml index 6b878a4682b..74912cf5fed 100644 --- a/target/docker/convert/velocyto_to_h5mu/.config.vsh.yaml +++ b/target/docker/convert/velocyto_to_h5mu/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "velocyto_to_h5mu" namespace: "convert" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -260,6 +260,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/velocyto_to_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/convert/velocyto_to_h5mu/velocyto_to_h5mu" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/convert/velocyto_to_h5mu/velocyto_to_h5mu b/target/docker/convert/velocyto_to_h5mu/velocyto_to_h5mu index c42ed34fc5f..9cbb067fc43 100755 --- a/target/docker/convert/velocyto_to_h5mu/velocyto_to_h5mu +++ b/target/docker/convert/velocyto_to_h5mu/velocyto_to_h5mu @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# velocyto_to_h5mu 1.0.1 +# velocyto_to_h5mu 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -175,7 +175,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "velocyto_to_h5mu 1.0.1" + echo "velocyto_to_h5mu 1.0.2" echo "" echo "Convert a velocyto loom file to a h5mu file." echo "" @@ -455,10 +455,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Robrecht Cannoodt, Angela Oliveira Pisco" LABEL org.opencontainers.image.description="Companion container for running component convert velocyto_to_h5mu" -LABEL org.opencontainers.image.created="2024-06-18T14:15:00Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:07Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -613,7 +613,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "velocyto_to_h5mu 1.0.1" + echo "velocyto_to_h5mu 1.0.2" exit ;; --input_loom) diff --git a/target/docker/correction/cellbender_remove_background/.config.vsh.yaml b/target/docker/correction/cellbender_remove_background/.config.vsh.yaml index fff5cfe4c5c..a2618c49166 100644 --- a/target/docker/correction/cellbender_remove_background/.config.vsh.yaml +++ b/target/docker/correction/cellbender_remove_background/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "cellbender_remove_background" namespace: "correction" - version: "1.0.1" + version: "1.0.2" argument_groups: - name: "Inputs" arguments: @@ -634,6 +634,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/correction/cellbender_remove_background" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/correction/cellbender_remove_background/cellbender_remove_background" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/correction/cellbender_remove_background/cellbender_remove_background b/target/docker/correction/cellbender_remove_background/cellbender_remove_background index 58fd95f9fce..61ffe710b7d 100755 --- a/target/docker/correction/cellbender_remove_background/cellbender_remove_background +++ b/target/docker/correction/cellbender_remove_background/cellbender_remove_background @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# cellbender_remove_background 1.0.1 +# cellbender_remove_background 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -170,7 +170,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "cellbender_remove_background 1.0.1" + echo "cellbender_remove_background 1.0.2" echo "" echo "Eliminating technical artifacts from high-throughput single-cell RNA sequencing" echo "data." @@ -686,10 +686,10 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "mudata~=0.2.1" "cellbender~=0.3.0" LABEL org.opencontainers.image.description="Companion container for running component correction cellbender_remove_background" -LABEL org.opencontainers.image.created="2024-06-18T14:14:59Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:07Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -844,7 +844,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "cellbender_remove_background 1.0.1" + echo "cellbender_remove_background 1.0.2" exit ;; --input) diff --git a/target/docker/correction/cellbender_remove_background_v0_2/.config.vsh.yaml b/target/docker/correction/cellbender_remove_background_v0_2/.config.vsh.yaml index 7a0fa13ff48..c20ba4e1bba 100644 --- a/target/docker/correction/cellbender_remove_background_v0_2/.config.vsh.yaml +++ b/target/docker/correction/cellbender_remove_background_v0_2/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "cellbender_remove_background_v0_2" namespace: "correction" - version: "1.0.1" + version: "1.0.2" argument_groups: - name: "Inputs" arguments: @@ -410,6 +410,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/correction/cellbender_remove_background_v0_2" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/correction/cellbender_remove_background_v0_2/cellbender_remove_background_v0_2" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/correction/cellbender_remove_background_v0_2/cellbender_remove_background_v0_2 b/target/docker/correction/cellbender_remove_background_v0_2/cellbender_remove_background_v0_2 index aa31dca20f2..ee96f58eeaa 100755 --- a/target/docker/correction/cellbender_remove_background_v0_2/cellbender_remove_background_v0_2 +++ b/target/docker/correction/cellbender_remove_background_v0_2/cellbender_remove_background_v0_2 @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# cellbender_remove_background_v0_2 1.0.1 +# cellbender_remove_background_v0_2 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -170,7 +170,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "cellbender_remove_background_v0_2 1.0.1" + echo "cellbender_remove_background_v0_2 1.0.2" echo "" echo "Eliminating technical artifacts from high-throughput single-cell RNA sequencing" echo "data." @@ -552,10 +552,10 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "anndata~=0.9.1" "mudata~=0.2.3" "pandas!=2.1.2" "muon==0.1.5" "tables==3.8.0" "cellbender==0.2.1" LABEL org.opencontainers.image.description="Companion container for running component correction cellbender_remove_background_v0_2" -LABEL org.opencontainers.image.created="2024-06-18T14:14:59Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:07Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -710,7 +710,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "cellbender_remove_background_v0_2 1.0.1" + echo "cellbender_remove_background_v0_2 1.0.2" exit ;; --input) diff --git a/target/docker/dataflow/concat/.config.vsh.yaml b/target/docker/dataflow/concat/.config.vsh.yaml index 5f4dc2e0769..9449e7a7c9b 100644 --- a/target/docker/dataflow/concat/.config.vsh.yaml +++ b/target/docker/dataflow/concat/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "concat" namespace: "dataflow" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -238,6 +238,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/dataflow/concat" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/dataflow/concat/concat" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/dataflow/concat/concat b/target/docker/dataflow/concat/concat index 8531c83eebe..bd4dd5aeee9 100755 --- a/target/docker/dataflow/concat/concat +++ b/target/docker/dataflow/concat/concat @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# concat 1.0.1 +# concat 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "concat 1.0.1" + echo "concat 1.0.2" echo "" echo "Concatenates several uni-modal samples in .h5mu files into a single file." echo "" @@ -452,10 +452,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component dataflow concat" -LABEL org.opencontainers.image.created="2024-06-18T14:14:56Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:08Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -610,7 +610,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "concat 1.0.1" + echo "concat 1.0.2" exit ;; --input) @@ -1257,7 +1257,15 @@ def split_conflicts_modalities(n_processes: int, samples: dict[str, anndata.AnnD output_index = getattr(output, matrix_name).index conflicts, concatenated_matrix = concatenate_matrices(n_processes, matrices, output_index) if concatenated_matrix.empty: - concatenated_matrix.index = output_index + concatenated_matrix.index = output_index + + # Even though we did not touch the varm and obsm matrices that were already present, + # the joining of observations might have caused a dtype change in these matrices as well + # so these also need to be casted to a writable dtype... + for multidim_name, multidim_data in getattr(output, f"{matrix_name}m").items(): + new_data = cast_to_writeable_dtype(multidim_data) if isinstance(multidim_data, pd.DataFrame) else multidim_data + getattr(output, f"{matrix_name}m")[multidim_name] = new_data + # Write the conflicts to the output for conflict_name, conflict_data in conflicts.items(): getattr(output, f"{matrix_name}m")[conflict_name] = conflict_data diff --git a/target/docker/dataflow/concatenate_h5mu/.config.vsh.yaml b/target/docker/dataflow/concatenate_h5mu/.config.vsh.yaml index 2c13cfa4a34..f685440b5e7 100644 --- a/target/docker/dataflow/concatenate_h5mu/.config.vsh.yaml +++ b/target/docker/dataflow/concatenate_h5mu/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "concatenate_h5mu" namespace: "dataflow" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -238,6 +238,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/dataflow/concatenate_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/dataflow/concatenate_h5mu/concatenate_h5mu" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/dataflow/concatenate_h5mu/concatenate_h5mu b/target/docker/dataflow/concatenate_h5mu/concatenate_h5mu index 79490401aa0..e7876e39a2a 100755 --- a/target/docker/dataflow/concatenate_h5mu/concatenate_h5mu +++ b/target/docker/dataflow/concatenate_h5mu/concatenate_h5mu @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# concatenate_h5mu 1.0.1 +# concatenate_h5mu 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "concatenate_h5mu 1.0.1" + echo "concatenate_h5mu 1.0.2" echo "" echo "Concatenates several uni-modal samples in .h5mu files into a single file." echo "" @@ -452,10 +452,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component dataflow concatenate_h5mu" -LABEL org.opencontainers.image.created="2024-06-18T14:14:56Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:08Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -610,7 +610,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "concatenate_h5mu 1.0.1" + echo "concatenate_h5mu 1.0.2" exit ;; --input) @@ -1257,7 +1257,15 @@ def split_conflicts_modalities(n_processes: int, samples: dict[str, anndata.AnnD output_index = getattr(output, matrix_name).index conflicts, concatenated_matrix = concatenate_matrices(n_processes, matrices, output_index) if concatenated_matrix.empty: - concatenated_matrix.index = output_index + concatenated_matrix.index = output_index + + # Even though we did not touch the varm and obsm matrices that were already present, + # the joining of observations might have caused a dtype change in these matrices as well + # so these also need to be casted to a writable dtype... + for multidim_name, multidim_data in getattr(output, f"{matrix_name}m").items(): + new_data = cast_to_writeable_dtype(multidim_data) if isinstance(multidim_data, pd.DataFrame) else multidim_data + getattr(output, f"{matrix_name}m")[multidim_name] = new_data + # Write the conflicts to the output for conflict_name, conflict_data in conflicts.items(): getattr(output, f"{matrix_name}m")[conflict_name] = conflict_data diff --git a/target/docker/dataflow/merge/.config.vsh.yaml b/target/docker/dataflow/merge/.config.vsh.yaml index 869cbd7423f..031a7520316 100644 --- a/target/docker/dataflow/merge/.config.vsh.yaml +++ b/target/docker/dataflow/merge/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "merge" namespace: "dataflow" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -187,6 +187,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/dataflow/merge" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/dataflow/merge/merge" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/dataflow/merge/merge b/target/docker/dataflow/merge/merge index db2b7ccd6bc..ffbf2767c01 100755 --- a/target/docker/dataflow/merge/merge +++ b/target/docker/dataflow/merge/merge @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# merge 1.0.1 +# merge 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "merge 1.0.1" + echo "merge 1.0.2" echo "" echo "Combine one or more single-modality .h5mu files together into one .h5mu file." echo "" @@ -424,10 +424,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component dataflow merge" -LABEL org.opencontainers.image.created="2024-06-18T14:14:56Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:07Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -582,7 +582,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "merge 1.0.1" + echo "merge 1.0.2" exit ;; --input) diff --git a/target/docker/dataflow/split_modalities/.config.vsh.yaml b/target/docker/dataflow/split_modalities/.config.vsh.yaml index 15eef5a9413..fd74b0ebdbd 100644 --- a/target/docker/dataflow/split_modalities/.config.vsh.yaml +++ b/target/docker/dataflow/split_modalities/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "split_modalities" namespace: "dataflow" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -213,6 +213,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/dataflow/split_modalities" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/dataflow/split_modalities/split_modalities" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/dataflow/split_modalities/split_modalities b/target/docker/dataflow/split_modalities/split_modalities index 3331ce2cce5..6430851e3f9 100755 --- a/target/docker/dataflow/split_modalities/split_modalities +++ b/target/docker/dataflow/split_modalities/split_modalities @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# split_modalities 1.0.1 +# split_modalities 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "split_modalities 1.0.1" + echo "split_modalities 1.0.2" echo "" echo "Split the modalities from a single .h5mu multimodal sample into seperate .h5mu" echo "files." @@ -431,10 +431,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component dataflow split_modalities" -LABEL org.opencontainers.image.created="2024-06-18T14:14:55Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:08Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -589,7 +589,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "split_modalities 1.0.1" + echo "split_modalities 1.0.2" exit ;; --input) diff --git a/target/docker/demux/bcl2fastq/.config.vsh.yaml b/target/docker/demux/bcl2fastq/.config.vsh.yaml index a312d015850..f83122a3268 100644 --- a/target/docker/demux/bcl2fastq/.config.vsh.yaml +++ b/target/docker/demux/bcl2fastq/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "bcl2fastq" namespace: "demux" - version: "1.0.1" + version: "1.0.2" authors: - name: "Toni Verbeiren" roles: @@ -177,6 +177,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/demux/bcl2fastq" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/demux/bcl2fastq/bcl2fastq" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/demux/bcl2fastq/bcl2fastq b/target/docker/demux/bcl2fastq/bcl2fastq index 2f42384acaa..b930305cb6f 100755 --- a/target/docker/demux/bcl2fastq/bcl2fastq +++ b/target/docker/demux/bcl2fastq/bcl2fastq @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# bcl2fastq 1.0.1 +# bcl2fastq 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "bcl2fastq 1.0.1" + echo "bcl2fastq 1.0.2" echo "" echo "Convert bcl files to fastq files using bcl2fastq." echo "" @@ -428,10 +428,10 @@ RUN apt-get update && \ LABEL org.opencontainers.image.authors="Toni Verbeiren" LABEL org.opencontainers.image.description="Companion container for running component demux bcl2fastq" -LABEL org.opencontainers.image.created="2024-06-18T14:14:57Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:07Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -586,7 +586,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bcl2fastq 1.0.1" + echo "bcl2fastq 1.0.2" exit ;; --input) diff --git a/target/docker/demux/bcl_convert/.config.vsh.yaml b/target/docker/demux/bcl_convert/.config.vsh.yaml index c3ca4785fae..819fa27b67b 100644 --- a/target/docker/demux/bcl_convert/.config.vsh.yaml +++ b/target/docker/demux/bcl_convert/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "bcl_convert" namespace: "demux" - version: "1.0.1" + version: "1.0.2" authors: - name: "Toni Verbeiren" roles: @@ -197,6 +197,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/demux/bcl_convert" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/demux/bcl_convert/bcl_convert" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/demux/bcl_convert/bcl_convert b/target/docker/demux/bcl_convert/bcl_convert index 44ba90ec1ab..017a47c7aab 100755 --- a/target/docker/demux/bcl_convert/bcl_convert +++ b/target/docker/demux/bcl_convert/bcl_convert @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# bcl_convert 1.0.1 +# bcl_convert 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "bcl_convert 1.0.1" + echo "bcl_convert 1.0.2" echo "" echo "Convert bcl files to fastq files using bcl-convert." echo "Information about upgrading from bcl2fastq via" @@ -435,10 +435,10 @@ RUN apt-get update && \ LABEL org.opencontainers.image.authors="Toni Verbeiren, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component demux bcl_convert" -LABEL org.opencontainers.image.created="2024-06-18T14:14:57Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:06Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -593,7 +593,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bcl_convert 1.0.1" + echo "bcl_convert 1.0.2" exit ;; --input) diff --git a/target/docker/demux/cellranger_mkfastq/.config.vsh.yaml b/target/docker/demux/cellranger_mkfastq/.config.vsh.yaml index 54641594cf4..072cb3593f7 100644 --- a/target/docker/demux/cellranger_mkfastq/.config.vsh.yaml +++ b/target/docker/demux/cellranger_mkfastq/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "cellranger_mkfastq" namespace: "demux" - version: "1.0.1" + version: "1.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -211,6 +211,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/demux/cellranger_mkfastq" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/demux/cellranger_mkfastq/cellranger_mkfastq" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/demux/cellranger_mkfastq/cellranger_mkfastq b/target/docker/demux/cellranger_mkfastq/cellranger_mkfastq index a458c8bde93..9c0a26b1e47 100755 --- a/target/docker/demux/cellranger_mkfastq/cellranger_mkfastq +++ b/target/docker/demux/cellranger_mkfastq/cellranger_mkfastq @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# cellranger_mkfastq 1.0.1 +# cellranger_mkfastq 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -175,7 +175,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "cellranger_mkfastq 1.0.1" + echo "cellranger_mkfastq 1.0.2" echo "" echo "Demultiplex raw sequencing data" echo "" @@ -433,10 +433,10 @@ apt upgrade -y && apt install -y procps && rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Samuel D'Souza, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component demux cellranger_mkfastq" -LABEL org.opencontainers.image.created="2024-06-18T14:14:57Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:06Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -591,7 +591,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "cellranger_mkfastq 1.0.1" + echo "cellranger_mkfastq 1.0.2" exit ;; --input) diff --git a/target/docker/dimred/pca/.config.vsh.yaml b/target/docker/dimred/pca/.config.vsh.yaml index fa7db00150b..533158ed03b 100644 --- a/target/docker/dimred/pca/.config.vsh.yaml +++ b/target/docker/dimred/pca/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "pca" namespace: "dimred" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries De Maeyer" roles: @@ -258,6 +258,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/dimred/pca" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/dimred/pca/pca" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/dimred/pca/pca b/target/docker/dimred/pca/pca index febc7088db7..fe83fe1904a 100755 --- a/target/docker/dimred/pca/pca +++ b/target/docker/dimred/pca/pca @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# pca 1.0.1 +# pca 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "pca 1.0.1" + echo "pca 1.0.2" echo "" echo "Computes PCA coordinates, loadings and variance decomposition. Uses the" echo "implementation of scikit-learn [Pedregosa11]." @@ -465,10 +465,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries De Maeyer" LABEL org.opencontainers.image.description="Companion container for running component dimred pca" -LABEL org.opencontainers.image.created="2024-06-18T14:15:01Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:06Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -623,7 +623,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "pca 1.0.1" + echo "pca 1.0.2" exit ;; --input) diff --git a/target/docker/dimred/tsne/.config.vsh.yaml b/target/docker/dimred/tsne/.config.vsh.yaml index 4c4918634ae..be643f1295a 100644 --- a/target/docker/dimred/tsne/.config.vsh.yaml +++ b/target/docker/dimred/tsne/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "tsne" namespace: "dimred" - version: "1.0.1" + version: "1.0.2" authors: - name: "Jakub Majercik" roles: @@ -311,6 +311,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/dimred/tsne" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/dimred/tsne/tsne" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/dimred/tsne/tsne b/target/docker/dimred/tsne/tsne index 1b94bccc075..27790a0c3a9 100755 --- a/target/docker/dimred/tsne/tsne +++ b/target/docker/dimred/tsne/tsne @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# tsne 1.0.1 +# tsne 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "tsne 1.0.1" + echo "tsne 1.0.2" echo "" echo "t-SNE (t-Distributed Stochastic Neighbor Embedding) is a dimensionality" echo "reduction technique used to visualize high-dimensional data in a low-dimensional" @@ -491,10 +491,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Jakub Majercik" LABEL org.opencontainers.image.description="Companion container for running component dimred tsne" -LABEL org.opencontainers.image.created="2024-06-18T14:15:01Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:05Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -649,7 +649,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "tsne 1.0.1" + echo "tsne 1.0.2" exit ;; --input) diff --git a/target/docker/dimred/umap/.config.vsh.yaml b/target/docker/dimred/umap/.config.vsh.yaml index 9956a838163..9b60eb2c30d 100644 --- a/target/docker/dimred/umap/.config.vsh.yaml +++ b/target/docker/dimred/umap/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "umap" namespace: "dimred" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries De Maeyer" roles: @@ -317,6 +317,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/dimred/umap" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/dimred/umap/umap" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/dimred/umap/umap b/target/docker/dimred/umap/umap index 48d268cae26..d54dda7bd0d 100755 --- a/target/docker/dimred/umap/umap +++ b/target/docker/dimred/umap/umap @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# umap 1.0.1 +# umap 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "umap 1.0.1" + echo "umap 1.0.2" echo "" echo "UMAP (Uniform Manifold Approximation and Projection) is a manifold learning" echo "technique suitable for visualizing high-dimensional data. Besides tending to be" @@ -502,10 +502,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries De Maeyer" LABEL org.opencontainers.image.description="Companion container for running component dimred umap" -LABEL org.opencontainers.image.created="2024-06-18T14:15:01Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:05Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -660,7 +660,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "umap 1.0.1" + echo "umap 1.0.2" exit ;; --input) diff --git a/target/docker/download/download_file/.config.vsh.yaml b/target/docker/download/download_file/.config.vsh.yaml index 5f57502c368..7d5d545db2d 100644 --- a/target/docker/download/download_file/.config.vsh.yaml +++ b/target/docker/download/download_file/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "download_file" namespace: "download" - version: "1.0.1" + version: "1.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -141,6 +141,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/download/download_file" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/download/download_file/download_file" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/download/download_file/download_file b/target/docker/download/download_file/download_file index dcba4b82ca5..6ecdc68f1a3 100755 --- a/target/docker/download/download_file/download_file +++ b/target/docker/download/download_file/download_file @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# download_file 1.0.1 +# download_file 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "download_file 1.0.1" + echo "download_file 1.0.2" echo "" echo "Download a file." echo "" @@ -424,10 +424,10 @@ ENTRYPOINT [] RUN : LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component download download_file" -LABEL org.opencontainers.image.created="2024-06-18T14:14:55Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:09Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -582,7 +582,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "download_file 1.0.1" + echo "download_file 1.0.2" exit ;; --input) diff --git a/target/docker/download/sync_test_resources/.config.vsh.yaml b/target/docker/download/sync_test_resources/.config.vsh.yaml index e4bde86d2f5..e5ccd6cebb4 100644 --- a/target/docker/download/sync_test_resources/.config.vsh.yaml +++ b/target/docker/download/sync_test_resources/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "sync_test_resources" namespace: "download" - version: "1.0.1" + version: "1.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -173,6 +173,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/download/sync_test_resources" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/download/sync_test_resources/sync_test_resources" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/download/sync_test_resources/sync_test_resources b/target/docker/download/sync_test_resources/sync_test_resources index 716ba55da1c..19a3636fd63 100755 --- a/target/docker/download/sync_test_resources/sync_test_resources +++ b/target/docker/download/sync_test_resources/sync_test_resources @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# sync_test_resources 1.0.1 +# sync_test_resources 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "sync_test_resources 1.0.1" + echo "sync_test_resources 1.0.2" echo "" echo "Synchronise the test resources from s3://openpipelines-data to resources_test" echo "" @@ -438,10 +438,10 @@ RUN yum install -y procps && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component download sync_test_resources" -LABEL org.opencontainers.image.created="2024-06-18T14:14:56Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:09Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -596,7 +596,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "sync_test_resources 1.0.1" + echo "sync_test_resources 1.0.2" exit ;; --input) diff --git a/target/docker/feature_annotation/highly_variable_features_scanpy/.config.vsh.yaml b/target/docker/feature_annotation/highly_variable_features_scanpy/.config.vsh.yaml index 8e6a67e1155..17eabc3ea1c 100644 --- a/target/docker/feature_annotation/highly_variable_features_scanpy/.config.vsh.yaml +++ b/target/docker/feature_annotation/highly_variable_features_scanpy/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "highly_variable_features_scanpy" namespace: "feature_annotation" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries De Maeyer" roles: @@ -352,6 +352,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/feature_annotation/highly_variable_features_scanpy" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/feature_annotation/highly_variable_features_scanpy/highly_variable_features_scanpy" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/feature_annotation/highly_variable_features_scanpy/highly_variable_features_scanpy b/target/docker/feature_annotation/highly_variable_features_scanpy/highly_variable_features_scanpy index b9304663e9b..318cef84276 100755 --- a/target/docker/feature_annotation/highly_variable_features_scanpy/highly_variable_features_scanpy +++ b/target/docker/feature_annotation/highly_variable_features_scanpy/highly_variable_features_scanpy @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# highly_variable_features_scanpy 1.0.1 +# highly_variable_features_scanpy 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "highly_variable_features_scanpy 1.0.1" + echo "highly_variable_features_scanpy 1.0.2" echo "" echo "Annotate highly variable features [Satija15] [Zheng17] [Stuart19]." echo "" @@ -524,10 +524,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries De Maeyer, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component feature_annotation highly_variable_features_scanpy" -LABEL org.opencontainers.image.created="2024-06-18T14:14:54Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:08Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -682,7 +682,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "highly_variable_features_scanpy 1.0.1" + echo "highly_variable_features_scanpy 1.0.2" exit ;; --input) diff --git a/target/docker/feature_annotation/score_genes_cell_cycle_scanpy/.config.vsh.yaml b/target/docker/feature_annotation/score_genes_cell_cycle_scanpy/.config.vsh.yaml index e4e387a0c6c..8d5d05c14b4 100644 --- a/target/docker/feature_annotation/score_genes_cell_cycle_scanpy/.config.vsh.yaml +++ b/target/docker/feature_annotation/score_genes_cell_cycle_scanpy/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "score_genes_cell_cycle_scanpy" namespace: "feature_annotation" - version: "1.0.1" + version: "1.0.2" authors: - name: "Robrecht Cannoodt" info: @@ -339,6 +339,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/feature_annotation/score_genes_cell_cycle_scanpy" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/feature_annotation/score_genes_cell_cycle_scanpy/score_genes_cell_cycle_scanpy" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/feature_annotation/score_genes_cell_cycle_scanpy/score_genes_cell_cycle_scanpy b/target/docker/feature_annotation/score_genes_cell_cycle_scanpy/score_genes_cell_cycle_scanpy index ec441db7027..f74b85e0fbc 100755 --- a/target/docker/feature_annotation/score_genes_cell_cycle_scanpy/score_genes_cell_cycle_scanpy +++ b/target/docker/feature_annotation/score_genes_cell_cycle_scanpy/score_genes_cell_cycle_scanpy @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# score_genes_cell_cycle_scanpy 1.0.1 +# score_genes_cell_cycle_scanpy 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "score_genes_cell_cycle_scanpy 1.0.1" + echo "score_genes_cell_cycle_scanpy 1.0.2" echo "" echo "Calculates the score associated to S phase and G2M phase and annotates the cell" echo "cycle phase for each cell, as implemented by scanpy." @@ -523,10 +523,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component feature_annotation score_genes_cell_cycle_scanpy" -LABEL org.opencontainers.image.created="2024-06-18T14:14:54Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:07Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -681,7 +681,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "score_genes_cell_cycle_scanpy 1.0.1" + echo "score_genes_cell_cycle_scanpy 1.0.2" exit ;; --input) diff --git a/target/docker/feature_annotation/score_genes_scanpy/.config.vsh.yaml b/target/docker/feature_annotation/score_genes_scanpy/.config.vsh.yaml index 43c17d033a6..651f11a75f7 100644 --- a/target/docker/feature_annotation/score_genes_scanpy/.config.vsh.yaml +++ b/target/docker/feature_annotation/score_genes_scanpy/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "score_genes_scanpy" namespace: "feature_annotation" - version: "1.0.1" + version: "1.0.2" authors: - name: "Robrecht Cannoodt" info: @@ -286,6 +286,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/feature_annotation/score_genes_scanpy" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/feature_annotation/score_genes_scanpy/score_genes_scanpy" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/feature_annotation/score_genes_scanpy/score_genes_scanpy b/target/docker/feature_annotation/score_genes_scanpy/score_genes_scanpy index af2246b3ae4..f7a134fa444 100755 --- a/target/docker/feature_annotation/score_genes_scanpy/score_genes_scanpy +++ b/target/docker/feature_annotation/score_genes_scanpy/score_genes_scanpy @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# score_genes_scanpy 1.0.1 +# score_genes_scanpy 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "score_genes_scanpy 1.0.1" + echo "score_genes_scanpy 1.0.2" echo "" echo "Calculates the score of a set of genes for each cell, as implemented by scanpy." echo "The score is the average expression of a set of genes subtracted with the" @@ -494,10 +494,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component feature_annotation score_genes_scanpy" -LABEL org.opencontainers.image.created="2024-06-18T14:14:55Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:08Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -652,7 +652,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "score_genes_scanpy 1.0.1" + echo "score_genes_scanpy 1.0.2" exit ;; --input) diff --git a/target/docker/files/make_params/.config.vsh.yaml b/target/docker/files/make_params/.config.vsh.yaml index 21dc3d01713..957c77cb413 100644 --- a/target/docker/files/make_params/.config.vsh.yaml +++ b/target/docker/files/make_params/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "make_params" namespace: "files" - version: "1.0.1" + version: "1.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -223,6 +223,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/files/make_params" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/files/make_params/make_params" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/files/make_params/make_params b/target/docker/files/make_params/make_params index ab85dba3d94..a516c37a671 100755 --- a/target/docker/files/make_params/make_params +++ b/target/docker/files/make_params/make_params @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# make_params 1.0.1 +# make_params 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "make_params 1.0.1" + echo "make_params 1.0.2" echo "" echo "Looks for files in a directory and turn it in a params file." echo "" @@ -444,10 +444,10 @@ ENTRYPOINT [] RUN : LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component files make_params" -LABEL org.opencontainers.image.created="2024-06-18T14:14:57Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:10Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -602,7 +602,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "make_params 1.0.1" + echo "make_params 1.0.2" exit ;; --base_dir) diff --git a/target/docker/filter/delimit_fraction/.config.vsh.yaml b/target/docker/filter/delimit_fraction/.config.vsh.yaml index 17769872622..e3775147a14 100644 --- a/target/docker/filter/delimit_fraction/.config.vsh.yaml +++ b/target/docker/filter/delimit_fraction/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "delimit_fraction" namespace: "filter" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -253,6 +253,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/filter/delimit_fraction" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/filter/delimit_fraction/delimit_fraction" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/filter/delimit_fraction/delimit_fraction b/target/docker/filter/delimit_fraction/delimit_fraction index 3e7234b2fad..35cb07f57b9 100755 --- a/target/docker/filter/delimit_fraction/delimit_fraction +++ b/target/docker/filter/delimit_fraction/delimit_fraction @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# delimit_fraction 1.0.1 +# delimit_fraction 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "delimit_fraction 1.0.1" + echo "delimit_fraction 1.0.2" echo "" echo "Turns a column containing values between 0 and 1 into a boolean column based on" echo "thresholds." @@ -460,10 +460,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component filter delimit_fraction" -LABEL org.opencontainers.image.created="2024-06-18T14:15:00Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:07Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -618,7 +618,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "delimit_fraction 1.0.1" + echo "delimit_fraction 1.0.2" exit ;; --input) diff --git a/target/docker/filter/do_filter/.config.vsh.yaml b/target/docker/filter/do_filter/.config.vsh.yaml index 937b7953f28..088dc21596b 100644 --- a/target/docker/filter/do_filter/.config.vsh.yaml +++ b/target/docker/filter/do_filter/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "do_filter" namespace: "filter" - version: "1.0.1" + version: "1.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -206,6 +206,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/filter/do_filter" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/filter/do_filter/do_filter" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/filter/do_filter/do_filter b/target/docker/filter/do_filter/do_filter index 264fe5a1dde..d167a307288 100755 --- a/target/docker/filter/do_filter/do_filter +++ b/target/docker/filter/do_filter/do_filter @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# do_filter 1.0.1 +# do_filter 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "do_filter 1.0.1" + echo "do_filter 1.0.2" echo "" echo "Remove observations and variables based on specified .obs and .var columns." echo "" @@ -438,10 +438,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component filter do_filter" -LABEL org.opencontainers.image.created="2024-06-18T14:15:00Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:07Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -596,7 +596,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "do_filter 1.0.1" + echo "do_filter 1.0.2" exit ;; --input) diff --git a/target/docker/filter/filter_with_counts/.config.vsh.yaml b/target/docker/filter/filter_with_counts/.config.vsh.yaml index a1ab419e76a..acda4d5d487 100644 --- a/target/docker/filter/filter_with_counts/.config.vsh.yaml +++ b/target/docker/filter/filter_with_counts/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "filter_with_counts" namespace: "filter" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries De Maeyer" roles: @@ -299,6 +299,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/filter/filter_with_counts" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/filter/filter_with_counts/filter_with_counts" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/filter/filter_with_counts/filter_with_counts b/target/docker/filter/filter_with_counts/filter_with_counts index d02110a66de..f3e262a3fbf 100755 --- a/target/docker/filter/filter_with_counts/filter_with_counts +++ b/target/docker/filter/filter_with_counts/filter_with_counts @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# filter_with_counts 1.0.1 +# filter_with_counts 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "filter_with_counts 1.0.1" + echo "filter_with_counts 1.0.2" echo "" echo "Filter scRNA-seq data based on the primary QC metrics." echo "This is based on both the UMI counts, the gene counts" @@ -478,10 +478,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries De Maeyer, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component filter filter_with_counts" -LABEL org.opencontainers.image.created="2024-06-18T14:15:00Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:06Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -636,7 +636,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "filter_with_counts 1.0.1" + echo "filter_with_counts 1.0.2" exit ;; --input) diff --git a/target/docker/filter/filter_with_hvg/.config.vsh.yaml b/target/docker/filter/filter_with_hvg/.config.vsh.yaml index 6af66efffdf..fdbe5ff37a7 100644 --- a/target/docker/filter/filter_with_hvg/.config.vsh.yaml +++ b/target/docker/filter/filter_with_hvg/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "filter_with_hvg" namespace: "filter" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries De Maeyer" roles: @@ -357,6 +357,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/filter/filter_with_hvg" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/filter/filter_with_hvg/filter_with_hvg" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/filter/filter_with_hvg/filter_with_hvg b/target/docker/filter/filter_with_hvg/filter_with_hvg index 8b144cd6110..7c7ce66f316 100755 --- a/target/docker/filter/filter_with_hvg/filter_with_hvg +++ b/target/docker/filter/filter_with_hvg/filter_with_hvg @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# filter_with_hvg 1.0.1 +# filter_with_hvg 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "filter_with_hvg 1.0.1" + echo "filter_with_hvg 1.0.2" echo "" echo "Annotate highly variable genes [Satija15] [Zheng17] [Stuart19]." echo "" @@ -524,10 +524,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries De Maeyer, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component filter filter_with_hvg" -LABEL org.opencontainers.image.created="2024-06-18T14:15:01Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:05Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -682,7 +682,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "filter_with_hvg 1.0.1" + echo "filter_with_hvg 1.0.2" exit ;; --input) diff --git a/target/docker/filter/filter_with_scrublet/.config.vsh.yaml b/target/docker/filter/filter_with_scrublet/.config.vsh.yaml index 6c9c7df1e19..f71a56d2ab1 100644 --- a/target/docker/filter/filter_with_scrublet/.config.vsh.yaml +++ b/target/docker/filter/filter_with_scrublet/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "filter_with_scrublet" namespace: "filter" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries De Maeyer" roles: @@ -319,6 +319,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/filter/filter_with_scrublet" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/filter/filter_with_scrublet/filter_with_scrublet" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/filter/filter_with_scrublet/filter_with_scrublet b/target/docker/filter/filter_with_scrublet/filter_with_scrublet index 0cf5192988f..7b4f65d8b78 100755 --- a/target/docker/filter/filter_with_scrublet/filter_with_scrublet +++ b/target/docker/filter/filter_with_scrublet/filter_with_scrublet @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# filter_with_scrublet 1.0.1 +# filter_with_scrublet 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "filter_with_scrublet 1.0.1" + echo "filter_with_scrublet 1.0.2" echo "" echo "Doublet detection using the Scrublet method (Wolock, Lopez and Klein, 2019)." echo "The method tests for potential doublets by using the expression profiles of" @@ -504,10 +504,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries De Maeyer, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component filter filter_with_scrublet" -LABEL org.opencontainers.image.created="2024-06-18T14:15:00Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:07Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -662,7 +662,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "filter_with_scrublet 1.0.1" + echo "filter_with_scrublet 1.0.2" exit ;; --input) diff --git a/target/docker/filter/intersect_obs/.config.vsh.yaml b/target/docker/filter/intersect_obs/.config.vsh.yaml index e9623d0dd46..80f3185803c 100644 --- a/target/docker/filter/intersect_obs/.config.vsh.yaml +++ b/target/docker/filter/intersect_obs/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "intersect_obs" namespace: "filter" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -193,6 +193,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/filter/intersect_obs" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/filter/intersect_obs/intersect_obs" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/filter/intersect_obs/intersect_obs b/target/docker/filter/intersect_obs/intersect_obs index a4e8ca2eacb..5f4a47f95bf 100755 --- a/target/docker/filter/intersect_obs/intersect_obs +++ b/target/docker/filter/intersect_obs/intersect_obs @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# intersect_obs 1.0.1 +# intersect_obs 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "intersect_obs 1.0.1" + echo "intersect_obs 1.0.2" echo "" echo "Create an intersection between two or more modalities." echo "" @@ -431,10 +431,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Isabelle Bergiers" LABEL org.opencontainers.image.description="Companion container for running component filter intersect_obs" -LABEL org.opencontainers.image.created="2024-06-18T14:14:59Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:06Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -589,7 +589,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "intersect_obs 1.0.1" + echo "intersect_obs 1.0.2" exit ;; --input) diff --git a/target/docker/filter/remove_modality/.config.vsh.yaml b/target/docker/filter/remove_modality/.config.vsh.yaml index 192b9979c1c..b2d57c1d389 100644 --- a/target/docker/filter/remove_modality/.config.vsh.yaml +++ b/target/docker/filter/remove_modality/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "remove_modality" namespace: "filter" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -175,6 +175,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/filter/remove_modality" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/filter/remove_modality/remove_modality" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/filter/remove_modality/remove_modality b/target/docker/filter/remove_modality/remove_modality index 978dca31dd0..6f260c398dc 100755 --- a/target/docker/filter/remove_modality/remove_modality +++ b/target/docker/filter/remove_modality/remove_modality @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# remove_modality 1.0.1 +# remove_modality 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "remove_modality 1.0.1" + echo "remove_modality 1.0.2" echo "" echo "Remove a modality from a .h5mu file" echo "" @@ -427,10 +427,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component filter remove_modality" -LABEL org.opencontainers.image.created="2024-06-18T14:14:59Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:06Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -585,7 +585,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "remove_modality 1.0.1" + echo "remove_modality 1.0.2" exit ;; --input) diff --git a/target/docker/filter/subset_h5mu/.config.vsh.yaml b/target/docker/filter/subset_h5mu/.config.vsh.yaml index b31a45229b7..b66375dcda0 100644 --- a/target/docker/filter/subset_h5mu/.config.vsh.yaml +++ b/target/docker/filter/subset_h5mu/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "subset_h5mu" namespace: "filter" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -191,6 +191,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/filter/subset_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/filter/subset_h5mu/subset_h5mu" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/filter/subset_h5mu/subset_h5mu b/target/docker/filter/subset_h5mu/subset_h5mu index a6232156384..400bcfc8dde 100755 --- a/target/docker/filter/subset_h5mu/subset_h5mu +++ b/target/docker/filter/subset_h5mu/subset_h5mu @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# subset_h5mu 1.0.1 +# subset_h5mu 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "subset_h5mu 1.0.1" + echo "subset_h5mu 1.0.2" echo "" echo "Create a subset of a mudata file by selecting the first number of observations" echo "" @@ -433,10 +433,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component filter subset_h5mu" -LABEL org.opencontainers.image.created="2024-06-18T14:14:59Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:06Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -591,7 +591,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "subset_h5mu 1.0.1" + echo "subset_h5mu 1.0.2" exit ;; --input) diff --git a/target/docker/genetic_demux/bcftools/.config.vsh.yaml b/target/docker/genetic_demux/bcftools/.config.vsh.yaml index ea008fd2251..59c55d9eccb 100644 --- a/target/docker/genetic_demux/bcftools/.config.vsh.yaml +++ b/target/docker/genetic_demux/bcftools/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "bcftools" namespace: "genetic_demux" - version: "1.0.1" + version: "1.0.2" authors: - name: "Xichen Wu" roles: @@ -179,6 +179,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/genetic_demux/bcftools" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/genetic_demux/bcftools/bcftools" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/genetic_demux/bcftools/bcftools b/target/docker/genetic_demux/bcftools/bcftools index 614b987fc2c..43351112965 100755 --- a/target/docker/genetic_demux/bcftools/bcftools +++ b/target/docker/genetic_demux/bcftools/bcftools @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# bcftools 1.0.1 +# bcftools 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "bcftools 1.0.1" + echo "bcftools 1.0.2" echo "" echo "Filter the variants called by freebayes or cellSNP" echo "" @@ -429,10 +429,10 @@ RUN apt-get update && \ RUN wget https://github.com/samtools/bcftools/releases/download/1.16/bcftools-1.16.tar.bz2 -O bcftools.tar.bz2 && tar -xjvf bcftools.tar.bz2 && cd bcftools-1.16 && make prefix=/usr/local install LABEL org.opencontainers.image.authors="Xichen Wu" LABEL org.opencontainers.image.description="Companion container for running component genetic_demux bcftools" -LABEL org.opencontainers.image.created="2024-06-18T14:14:57Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:10Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -587,7 +587,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bcftools 1.0.1" + echo "bcftools 1.0.2" exit ;; --vcf) diff --git a/target/docker/genetic_demux/cellsnp/.config.vsh.yaml b/target/docker/genetic_demux/cellsnp/.config.vsh.yaml index 74c83203d6d..05d49334042 100644 --- a/target/docker/genetic_demux/cellsnp/.config.vsh.yaml +++ b/target/docker/genetic_demux/cellsnp/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "cellsnp" namespace: "genetic_demux" - version: "1.0.1" + version: "1.0.2" authors: - name: "Xichen Wu" roles: @@ -374,6 +374,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/genetic_demux/cellsnp" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/genetic_demux/cellsnp/cellsnp" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/genetic_demux/cellsnp/cellsnp b/target/docker/genetic_demux/cellsnp/cellsnp index 38932280994..e0295f87b8f 100755 --- a/target/docker/genetic_demux/cellsnp/cellsnp +++ b/target/docker/genetic_demux/cellsnp/cellsnp @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# cellsnp 1.0.1 +# cellsnp 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "cellsnp 1.0.1" + echo "cellsnp 1.0.2" echo "" echo "cellSNP aims to pileup the expressed alleles in single-cell or bulk RNA-seq" echo "data. It can be directly used for donor deconvolution in multiplexed single-cell" @@ -515,10 +515,10 @@ RUN wget https://github.com/samtools/htslib/releases/download/1.16/htslib-1.16.t RUN git clone https://github.com/single-cell-genetics/cellsnp-lite.git && cd cellsnp-lite && autoreconf -iv && ./configure --with-htslib=/htslib-1.16 && make && make install LABEL org.opencontainers.image.authors="Xichen Wu" LABEL org.opencontainers.image.description="Companion container for running component genetic_demux cellsnp" -LABEL org.opencontainers.image.created="2024-06-18T14:14:55Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:08Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -673,7 +673,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "cellsnp 1.0.1" + echo "cellsnp 1.0.2" exit ;; --sam_file) diff --git a/target/docker/genetic_demux/demuxlet/.config.vsh.yaml b/target/docker/genetic_demux/demuxlet/.config.vsh.yaml index f26d5f8b645..18cdc5f8dc8 100644 --- a/target/docker/genetic_demux/demuxlet/.config.vsh.yaml +++ b/target/docker/genetic_demux/demuxlet/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "demuxlet" namespace: "genetic_demux" - version: "1.0.1" + version: "1.0.2" authors: - name: "Xichen Wu" roles: @@ -459,6 +459,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/genetic_demux/demuxlet" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/genetic_demux/demuxlet/demuxlet" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/genetic_demux/demuxlet/demuxlet b/target/docker/genetic_demux/demuxlet/demuxlet index 269c656e569..a7e1f864ca7 100755 --- a/target/docker/genetic_demux/demuxlet/demuxlet +++ b/target/docker/genetic_demux/demuxlet/demuxlet @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# demuxlet 1.0.1 +# demuxlet 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "demuxlet 1.0.1" + echo "demuxlet 1.0.2" echo "" echo "Demuxlet is a software tool to deconvolute sample identity and identify" echo "multiplets when" @@ -560,10 +560,10 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag LABEL org.opencontainers.image.authors="Xichen Wu" LABEL org.opencontainers.image.description="Companion container for running component genetic_demux demuxlet" -LABEL org.opencontainers.image.created="2024-06-18T14:14:57Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:09Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -718,7 +718,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "demuxlet 1.0.1" + echo "demuxlet 1.0.2" exit ;; --sam) diff --git a/target/docker/genetic_demux/dsc_pileup/.config.vsh.yaml b/target/docker/genetic_demux/dsc_pileup/.config.vsh.yaml index 13e562ef8d3..d51408e727e 100644 --- a/target/docker/genetic_demux/dsc_pileup/.config.vsh.yaml +++ b/target/docker/genetic_demux/dsc_pileup/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "dsc_pileup" namespace: "genetic_demux" - version: "1.0.1" + version: "1.0.2" authors: - name: "Xichen Wu" roles: @@ -370,6 +370,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/genetic_demux/dsc_pileup" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/genetic_demux/dsc_pileup/dsc_pileup" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/genetic_demux/dsc_pileup/dsc_pileup b/target/docker/genetic_demux/dsc_pileup/dsc_pileup index aa0c01a74b5..4bcce2e9745 100755 --- a/target/docker/genetic_demux/dsc_pileup/dsc_pileup +++ b/target/docker/genetic_demux/dsc_pileup/dsc_pileup @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# dsc_pileup 1.0.1 +# dsc_pileup 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "dsc_pileup 1.0.1" + echo "dsc_pileup 1.0.2" echo "" echo "Dsc-pileup is a software tool to pileup reads and corresponding base quality" echo "for each overlapping SNPs and each barcode. By using pileup files," @@ -515,10 +515,10 @@ RUN git clone https://github.com/samtools/htslib.git /tmp/htslib && cd /tmp/htsl RUN git clone --depth 1 https://github.com/statgen/popscle.git /tmp/popscle && mkdir -p /tmp/popscle/build && cd /tmp/popscle/build && cmake .. && make && cp /tmp/popscle/bin/popscle /usr/local/bin LABEL org.opencontainers.image.authors="Xichen Wu" LABEL org.opencontainers.image.description="Companion container for running component genetic_demux dsc_pileup" -LABEL org.opencontainers.image.created="2024-06-18T14:14:57Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:07Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -673,7 +673,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "dsc_pileup 1.0.1" + echo "dsc_pileup 1.0.2" exit ;; --sam) diff --git a/target/docker/genetic_demux/freebayes/.config.vsh.yaml b/target/docker/genetic_demux/freebayes/.config.vsh.yaml index d2a8de866a0..1564d11ebcc 100644 --- a/target/docker/genetic_demux/freebayes/.config.vsh.yaml +++ b/target/docker/genetic_demux/freebayes/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "freebayes" namespace: "genetic_demux" - version: "1.0.1" + version: "1.0.2" authors: - name: "Xichen Wu" roles: @@ -853,6 +853,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/genetic_demux/freebayes" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/genetic_demux/freebayes/freebayes" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/genetic_demux/freebayes/freebayes b/target/docker/genetic_demux/freebayes/freebayes index ddc71f688ee..712c129f166 100755 --- a/target/docker/genetic_demux/freebayes/freebayes +++ b/target/docker/genetic_demux/freebayes/freebayes @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# freebayes 1.0.1 +# freebayes 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "freebayes 1.0.1" + echo "freebayes 1.0.2" echo "" echo "Freebayes is a Bayesian genetic variant detector designed to" echo "find small polymorphisms, specifically SNPs." @@ -800,10 +800,10 @@ RUN apt-get update && \ LABEL org.opencontainers.image.authors="Xichen Wu" LABEL org.opencontainers.image.description="Companion container for running component genetic_demux freebayes" -LABEL org.opencontainers.image.created="2024-06-18T14:14:54Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:09Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -958,7 +958,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "freebayes 1.0.1" + echo "freebayes 1.0.2" exit ;; --bam) diff --git a/target/docker/genetic_demux/freemuxlet/.config.vsh.yaml b/target/docker/genetic_demux/freemuxlet/.config.vsh.yaml index e966c64805c..cbeb3ba04b1 100644 --- a/target/docker/genetic_demux/freemuxlet/.config.vsh.yaml +++ b/target/docker/genetic_demux/freemuxlet/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "freemuxlet" namespace: "genetic_demux" - version: "1.0.1" + version: "1.0.2" authors: - name: "Xichen Wu" roles: @@ -367,6 +367,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/genetic_demux/freemuxlet" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/genetic_demux/freemuxlet/freemuxlet" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/genetic_demux/freemuxlet/freemuxlet b/target/docker/genetic_demux/freemuxlet/freemuxlet index 6d3b6c86b8a..8dcd7fbe289 100755 --- a/target/docker/genetic_demux/freemuxlet/freemuxlet +++ b/target/docker/genetic_demux/freemuxlet/freemuxlet @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# freemuxlet 1.0.1 +# freemuxlet 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "freemuxlet 1.0.1" + echo "freemuxlet 1.0.2" echo "" echo "Freemuxlet is a software tool to deconvolute sample identity and identify" echo "multiplets when" @@ -520,10 +520,10 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag LABEL org.opencontainers.image.authors="Xichen Wu" LABEL org.opencontainers.image.description="Companion container for running component genetic_demux freemuxlet" -LABEL org.opencontainers.image.created="2024-06-18T14:14:58Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:08Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -678,7 +678,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "freemuxlet 1.0.1" + echo "freemuxlet 1.0.2" exit ;; --plp) diff --git a/target/docker/genetic_demux/samtools/.config.vsh.yaml b/target/docker/genetic_demux/samtools/.config.vsh.yaml index 9e0ed6884c7..74fb813351a 100644 --- a/target/docker/genetic_demux/samtools/.config.vsh.yaml +++ b/target/docker/genetic_demux/samtools/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "samtools" namespace: "genetic_demux" - version: "1.0.1" + version: "1.0.2" authors: - name: "Xichen Wu" roles: @@ -154,6 +154,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/genetic_demux/samtools" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/genetic_demux/samtools/samtools" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/genetic_demux/samtools/samtools b/target/docker/genetic_demux/samtools/samtools index 47ca4231774..882912f07c0 100755 --- a/target/docker/genetic_demux/samtools/samtools +++ b/target/docker/genetic_demux/samtools/samtools @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# samtools 1.0.1 +# samtools 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "samtools 1.0.1" + echo "samtools 1.0.2" echo "" echo "Filter the BAM according to the instruction of scSplit via Samtools." echo "" @@ -418,10 +418,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Xichen Wu" LABEL org.opencontainers.image.description="Companion container for running component genetic_demux samtools" -LABEL org.opencontainers.image.created="2024-06-18T14:14:55Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:08Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -576,7 +576,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "samtools 1.0.1" + echo "samtools 1.0.2" exit ;; --bam) diff --git a/target/docker/genetic_demux/scsplit/.config.vsh.yaml b/target/docker/genetic_demux/scsplit/.config.vsh.yaml index dae2d0f526a..e6066659b89 100644 --- a/target/docker/genetic_demux/scsplit/.config.vsh.yaml +++ b/target/docker/genetic_demux/scsplit/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "scsplit" namespace: "genetic_demux" - version: "1.0.1" + version: "1.0.2" authors: - name: "Xichen Wu" roles: @@ -293,6 +293,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/genetic_demux/scsplit" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/genetic_demux/scsplit/scsplit" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/genetic_demux/scsplit/scsplit b/target/docker/genetic_demux/scsplit/scsplit index 0ed3c073280..d7c3842bf36 100755 --- a/target/docker/genetic_demux/scsplit/scsplit +++ b/target/docker/genetic_demux/scsplit/scsplit @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# scsplit 1.0.1 +# scsplit 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "scsplit 1.0.1" + echo "scsplit 1.0.2" echo "" echo "scsplit is a genotype-free demultiplexing methode of pooled single-cell RNA-seq," echo "using a hidden state model for identifying genetically distinct samples within a" @@ -480,10 +480,10 @@ RUN pip install --upgrade pip && \ RUN git clone https://github.com/jon-xu/scSplit && cp scSplit/scSplit /usr/local/bin && rm -rf scSplit LABEL org.opencontainers.image.authors="Xichen Wu" LABEL org.opencontainers.image.description="Companion container for running component genetic_demux scsplit" -LABEL org.opencontainers.image.created="2024-06-18T14:14:56Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:09Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -638,7 +638,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "scsplit 1.0.1" + echo "scsplit 1.0.2" exit ;; --vcf) diff --git a/target/docker/genetic_demux/souporcell/.config.vsh.yaml b/target/docker/genetic_demux/souporcell/.config.vsh.yaml index 699c58d6012..8bb7819486a 100644 --- a/target/docker/genetic_demux/souporcell/.config.vsh.yaml +++ b/target/docker/genetic_demux/souporcell/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "souporcell" namespace: "genetic_demux" - version: "1.0.1" + version: "1.0.2" authors: - name: "Xichen Wu" roles: @@ -282,6 +282,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/genetic_demux/souporcell" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/genetic_demux/souporcell/souporcell" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/genetic_demux/souporcell/souporcell b/target/docker/genetic_demux/souporcell/souporcell index f1447a58433..83f5d22cb77 100755 --- a/target/docker/genetic_demux/souporcell/souporcell +++ b/target/docker/genetic_demux/souporcell/souporcell @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# souporcell 1.0.1 +# souporcell 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "souporcell 1.0.1" + echo "souporcell 1.0.2" echo "" echo "souporcell is a method for clustering mixed-genotype scRNAseq experiments by" echo "individual." @@ -478,10 +478,10 @@ ENTRYPOINT [] RUN : LABEL org.opencontainers.image.authors="Xichen Wu" LABEL org.opencontainers.image.description="Companion container for running component genetic_demux souporcell" -LABEL org.opencontainers.image.created="2024-06-18T14:14:56Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:08Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -636,7 +636,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "souporcell 1.0.1" + echo "souporcell 1.0.2" exit ;; --fasta) diff --git a/target/docker/genetic_demux/vireo/.config.vsh.yaml b/target/docker/genetic_demux/vireo/.config.vsh.yaml index 18fcf91d9d1..697563d4a8c 100644 --- a/target/docker/genetic_demux/vireo/.config.vsh.yaml +++ b/target/docker/genetic_demux/vireo/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "vireo" namespace: "genetic_demux" - version: "1.0.1" + version: "1.0.2" authors: - name: "Xichen Wu" roles: @@ -302,6 +302,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/genetic_demux/vireo" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/genetic_demux/vireo/vireo" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/genetic_demux/vireo/vireo b/target/docker/genetic_demux/vireo/vireo index 1370a663a19..aba51302617 100755 --- a/target/docker/genetic_demux/vireo/vireo +++ b/target/docker/genetic_demux/vireo/vireo @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# vireo 1.0.1 +# vireo 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "vireo 1.0.1" + echo "vireo 1.0.2" echo "" echo "Vireo is primarily designed for demultiplexing cells into donors by modelling of" echo "expressed alleles." @@ -485,10 +485,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Xichen Wu" LABEL org.opencontainers.image.description="Companion container for running component genetic_demux vireo" -LABEL org.opencontainers.image.created="2024-06-18T14:14:57Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:09Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -643,7 +643,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "vireo 1.0.1" + echo "vireo 1.0.2" exit ;; --cell_data) diff --git a/target/docker/integrate/harmonypy/.config.vsh.yaml b/target/docker/integrate/harmonypy/.config.vsh.yaml index 3ca80e6db6a..8281a0784fc 100644 --- a/target/docker/integrate/harmonypy/.config.vsh.yaml +++ b/target/docker/integrate/harmonypy/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "harmonypy" namespace: "integrate" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -245,6 +245,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/integrate/harmonypy" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/integrate/harmonypy/harmonypy" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/integrate/harmonypy/harmonypy b/target/docker/integrate/harmonypy/harmonypy index daa238e30c1..3ff13a22a7f 100755 --- a/target/docker/integrate/harmonypy/harmonypy +++ b/target/docker/integrate/harmonypy/harmonypy @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# harmonypy 1.0.1 +# harmonypy 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "harmonypy 1.0.1" + echo "harmonypy 1.0.2" echo "" echo "Performs Harmony integration based as described in" echo "https://github.com/immunogenomics/harmony. Based on an implementation in python" @@ -451,10 +451,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component integrate harmonypy" -LABEL org.opencontainers.image.created="2024-06-18T14:14:59Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:09Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -609,7 +609,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "harmonypy 1.0.1" + echo "harmonypy 1.0.2" exit ;; --input) diff --git a/target/docker/integrate/scanorama/.config.vsh.yaml b/target/docker/integrate/scanorama/.config.vsh.yaml index 24b9fc50bcc..672c4532c18 100644 --- a/target/docker/integrate/scanorama/.config.vsh.yaml +++ b/target/docker/integrate/scanorama/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "scanorama" namespace: "integrate" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries De Maeyer" roles: @@ -288,6 +288,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/integrate/scanorama" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/integrate/scanorama/scanorama" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/integrate/scanorama/scanorama b/target/docker/integrate/scanorama/scanorama index 93aae2b5d36..9325f5c2067 100755 --- a/target/docker/integrate/scanorama/scanorama +++ b/target/docker/integrate/scanorama/scanorama @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# scanorama 1.0.1 +# scanorama 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "scanorama 1.0.1" + echo "scanorama 1.0.2" echo "" echo "Use Scanorama to integrate different experiments." echo "" @@ -472,10 +472,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries De Maeyer, Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component integrate scanorama" -LABEL org.opencontainers.image.created="2024-06-18T14:14:59Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:08Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -630,7 +630,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "scanorama 1.0.1" + echo "scanorama 1.0.2" exit ;; --input) diff --git a/target/docker/integrate/scarches/.config.vsh.yaml b/target/docker/integrate/scarches/.config.vsh.yaml index b9582f51929..a0af5c4c6d9 100644 --- a/target/docker/integrate/scarches/.config.vsh.yaml +++ b/target/docker/integrate/scarches/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "scarches" namespace: "integrate" - version: "1.0.1" + version: "1.0.2" authors: - name: "Vladimir Shitov" info: @@ -336,6 +336,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/integrate/scarches" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/integrate/scarches/scarches" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/integrate/scarches/scarches b/target/docker/integrate/scarches/scarches index fa51ff8bf72..4daeb6651d1 100755 --- a/target/docker/integrate/scarches/scarches +++ b/target/docker/integrate/scarches/scarches @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# scarches 1.0.1 +# scarches 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "scarches 1.0.1" + echo "scarches 1.0.2" echo "" echo "Performs reference mapping with scArches" echo "" @@ -496,10 +496,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Vladimir Shitov" LABEL org.opencontainers.image.description="Companion container for running component integrate scarches" -LABEL org.opencontainers.image.created="2024-06-18T14:14:59Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:07Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -654,7 +654,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "scarches 1.0.1" + echo "scarches 1.0.2" exit ;; --input) diff --git a/target/docker/integrate/scvi/.config.vsh.yaml b/target/docker/integrate/scvi/.config.vsh.yaml index 715db7f54c1..986144432de 100644 --- a/target/docker/integrate/scvi/.config.vsh.yaml +++ b/target/docker/integrate/scvi/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "scvi" namespace: "integrate" - version: "1.0.1" + version: "1.0.2" authors: - name: "Malte D. Luecken" roles: @@ -594,6 +594,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/integrate/scvi" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/integrate/scvi/scvi" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/integrate/scvi/scvi b/target/docker/integrate/scvi/scvi index cf62be8fd8b..476871829b0 100755 --- a/target/docker/integrate/scvi/scvi +++ b/target/docker/integrate/scvi/scvi @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# scvi 1.0.1 +# scvi 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -175,7 +175,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "scvi 1.0.1" + echo "scvi 1.0.2" echo "" echo "Performs scvi integration as done in the human lung cell atlas" echo "https://github.com/LungCellAtlas/HLCA" @@ -627,10 +627,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Malte D. Luecken, Dries Schaumont, Matthias Beyens" LABEL org.opencontainers.image.description="Companion container for running component integrate scvi" -LABEL org.opencontainers.image.created="2024-06-18T14:15:01Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:08Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -785,7 +785,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "scvi 1.0.1" + echo "scvi 1.0.2" exit ;; --input) diff --git a/target/docker/integrate/totalvi/.config.vsh.yaml b/target/docker/integrate/totalvi/.config.vsh.yaml index ae48e01c6bb..6ab86a4658b 100644 --- a/target/docker/integrate/totalvi/.config.vsh.yaml +++ b/target/docker/integrate/totalvi/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "totalvi" namespace: "integrate" - version: "1.0.1" + version: "1.0.2" authors: - name: "Vladimir Shitov" info: @@ -353,6 +353,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/integrate/totalvi" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/integrate/totalvi/totalvi" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/integrate/totalvi/totalvi b/target/docker/integrate/totalvi/totalvi index 44e53360f04..88e473acacd 100755 --- a/target/docker/integrate/totalvi/totalvi +++ b/target/docker/integrate/totalvi/totalvi @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# totalvi 1.0.1 +# totalvi 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "totalvi 1.0.1" + echo "totalvi 1.0.2" echo "" echo "Performs mapping to the reference by totalvi model:" echo "https://docs.scvi-tools.org/en/stable/tutorials/notebooks/scarches_scvi_tools.html#Reference-mapping-with-TOTALVI" @@ -500,10 +500,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Vladimir Shitov" LABEL org.opencontainers.image.description="Companion container for running component integrate totalvi" -LABEL org.opencontainers.image.created="2024-06-18T14:14:58Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:08Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -658,7 +658,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "totalvi 1.0.1" + echo "totalvi 1.0.2" exit ;; --input) diff --git a/target/docker/interactive/run_cellxgene/.config.vsh.yaml b/target/docker/interactive/run_cellxgene/.config.vsh.yaml index 520d0967092..ed842134128 100644 --- a/target/docker/interactive/run_cellxgene/.config.vsh.yaml +++ b/target/docker/interactive/run_cellxgene/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "run_cellxgene" namespace: "interactive" - version: "1.0.1" + version: "1.0.2" arguments: - type: "file" name: "--input" @@ -85,6 +85,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/interactive/run_cellxgene" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/interactive/run_cellxgene/run_cellxgene" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/interactive/run_cellxgene/run_cellxgene b/target/docker/interactive/run_cellxgene/run_cellxgene index 25540ab81f1..1e31a4656ca 100755 --- a/target/docker/interactive/run_cellxgene/run_cellxgene +++ b/target/docker/interactive/run_cellxgene/run_cellxgene @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# run_cellxgene 1.0.1 +# run_cellxgene 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -170,7 +170,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "run_cellxgene 1.0.1" + echo "run_cellxgene 1.0.2" echo "" echo "" echo "" @@ -415,10 +415,10 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "cellxgene" LABEL org.opencontainers.image.description="Companion container for running component interactive run_cellxgene" -LABEL org.opencontainers.image.created="2024-06-18T14:14:59Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:05Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -573,7 +573,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "run_cellxgene 1.0.1" + echo "run_cellxgene 1.0.2" exit ;; --input) diff --git a/target/docker/interactive/run_cirrocumulus/.config.vsh.yaml b/target/docker/interactive/run_cirrocumulus/.config.vsh.yaml index 02f140aa7d1..114c64f3cdf 100644 --- a/target/docker/interactive/run_cirrocumulus/.config.vsh.yaml +++ b/target/docker/interactive/run_cirrocumulus/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "run_cirrocumulus" namespace: "interactive" - version: "1.0.1" + version: "1.0.2" arguments: - type: "file" name: "--input" @@ -87,6 +87,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/interactive/run_cirrocumulus" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/interactive/run_cirrocumulus/run_cirrocumulus" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/interactive/run_cirrocumulus/run_cirrocumulus b/target/docker/interactive/run_cirrocumulus/run_cirrocumulus index f39affcba7f..d59a2713332 100755 --- a/target/docker/interactive/run_cirrocumulus/run_cirrocumulus +++ b/target/docker/interactive/run_cirrocumulus/run_cirrocumulus @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# run_cirrocumulus 1.0.1 +# run_cirrocumulus 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -170,7 +170,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "run_cirrocumulus 1.0.1" + echo "run_cirrocumulus 1.0.2" echo "" echo "" echo "" @@ -415,10 +415,10 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "requests" "aiohttp" "cirrocumulus" LABEL org.opencontainers.image.description="Companion container for running component interactive run_cirrocumulus" -LABEL org.opencontainers.image.created="2024-06-18T14:14:59Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:05Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -573,7 +573,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "run_cirrocumulus 1.0.1" + echo "run_cirrocumulus 1.0.2" exit ;; --input) diff --git a/target/docker/interpret/lianapy/.config.vsh.yaml b/target/docker/interpret/lianapy/.config.vsh.yaml index cc7b95efdbd..83d999dd253 100644 --- a/target/docker/interpret/lianapy/.config.vsh.yaml +++ b/target/docker/interpret/lianapy/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "lianapy" namespace: "interpret" - version: "1.0.1" + version: "1.0.2" authors: - name: "Mauro Saporita" roles: @@ -317,6 +317,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/interpret/lianapy" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/interpret/lianapy/lianapy" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/interpret/lianapy/lianapy b/target/docker/interpret/lianapy/lianapy index e50132c71f0..11e072b4094 100755 --- a/target/docker/interpret/lianapy/lianapy +++ b/target/docker/interpret/lianapy/lianapy @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# lianapy 1.0.1 +# lianapy 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "lianapy 1.0.1" + echo "lianapy 1.0.2" echo "" echo "Performs LIANA integration based as described in" echo "https://github.com/saezlab/liana-py" @@ -485,10 +485,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Mauro Saporita, Povilas Gibas" LABEL org.opencontainers.image.description="Companion container for running component interpret lianapy" -LABEL org.opencontainers.image.created="2024-06-18T14:15:01Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:12Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -643,7 +643,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "lianapy 1.0.1" + echo "lianapy 1.0.2" exit ;; --input) diff --git a/target/docker/labels_transfer/knn/.config.vsh.yaml b/target/docker/labels_transfer/knn/.config.vsh.yaml index 91b6d7b3bce..e36e098379e 100644 --- a/target/docker/labels_transfer/knn/.config.vsh.yaml +++ b/target/docker/labels_transfer/knn/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "knn" namespace: "labels_transfer" - version: "1.0.1" + version: "1.0.2" authors: - name: "Vladimir Shitov" roles: @@ -384,6 +384,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/labels_transfer/knn" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/labels_transfer/knn/knn" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/labels_transfer/knn/knn b/target/docker/labels_transfer/knn/knn index 10202e5d2db..17e6a479364 100755 --- a/target/docker/labels_transfer/knn/knn +++ b/target/docker/labels_transfer/knn/knn @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# knn 1.0.1 +# knn 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "knn 1.0.1" + echo "knn 1.0.2" echo "" echo "Performs label transfer from reference to query using KNN classifier" echo "" @@ -483,10 +483,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Vladimir Shitov" LABEL org.opencontainers.image.description="Companion container for running component labels_transfer knn" -LABEL org.opencontainers.image.created="2024-06-18T14:14:57Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:09Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "knn 1.0.1" + echo "knn 1.0.2" exit ;; --input) diff --git a/target/docker/labels_transfer/xgboost/.config.vsh.yaml b/target/docker/labels_transfer/xgboost/.config.vsh.yaml index 81c4593336d..097cfcc2b3f 100644 --- a/target/docker/labels_transfer/xgboost/.config.vsh.yaml +++ b/target/docker/labels_transfer/xgboost/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "xgboost" namespace: "labels_transfer" - version: "1.0.1" + version: "1.0.2" authors: - name: "Vladimir Shitov" roles: @@ -599,6 +599,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/labels_transfer/xgboost" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/labels_transfer/xgboost/xgboost" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/labels_transfer/xgboost/xgboost b/target/docker/labels_transfer/xgboost/xgboost index fbf857397de..73f273365ce 100755 --- a/target/docker/labels_transfer/xgboost/xgboost +++ b/target/docker/labels_transfer/xgboost/xgboost @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# xgboost 1.0.1 +# xgboost 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "xgboost 1.0.1" + echo "xgboost 1.0.2" echo "" echo "Performs label transfer from reference to query using XGBoost classifier" echo "" @@ -610,10 +610,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Vladimir Shitov" LABEL org.opencontainers.image.description="Companion container for running component labels_transfer xgboost" -LABEL org.opencontainers.image.created="2024-06-18T14:14:57Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:09Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -768,7 +768,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "xgboost 1.0.1" + echo "xgboost 1.0.2" exit ;; --input) diff --git a/target/docker/mapping/bd_rhapsody/.config.vsh.yaml b/target/docker/mapping/bd_rhapsody/.config.vsh.yaml index ad7429675a2..5e460d0d1bb 100644 --- a/target/docker/mapping/bd_rhapsody/.config.vsh.yaml +++ b/target/docker/mapping/bd_rhapsody/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "bd_rhapsody" namespace: "mapping" - version: "1.0.1" + version: "1.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -420,6 +420,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/bd_rhapsody" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/bd_rhapsody/bd_rhapsody" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/mapping/bd_rhapsody/bd_rhapsody b/target/docker/mapping/bd_rhapsody/bd_rhapsody index cf34acba4ca..94d46802cb1 100755 --- a/target/docker/mapping/bd_rhapsody/bd_rhapsody +++ b/target/docker/mapping/bd_rhapsody/bd_rhapsody @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# bd_rhapsody 1.0.1 +# bd_rhapsody 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "bd_rhapsody 1.0.1" + echo "bd_rhapsody 1.0.2" echo "" echo "A wrapper for the BD Rhapsody Analysis CWL v1.10.1 pipeline." echo "" @@ -547,10 +547,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component mapping bd_rhapsody" -LABEL org.opencontainers.image.created="2024-06-18T14:14:55Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:05Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -705,7 +705,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bd_rhapsody 1.0.1" + echo "bd_rhapsody 1.0.2" exit ;; --mode) diff --git a/target/docker/mapping/cellranger_count/.config.vsh.yaml b/target/docker/mapping/cellranger_count/.config.vsh.yaml index 59f1b8e9430..91339bfd304 100644 --- a/target/docker/mapping/cellranger_count/.config.vsh.yaml +++ b/target/docker/mapping/cellranger_count/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "cellranger_count" namespace: "mapping" - version: "1.0.1" + version: "1.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -270,6 +270,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/cellranger_count" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/cellranger_count/cellranger_count" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/mapping/cellranger_count/cellranger_count b/target/docker/mapping/cellranger_count/cellranger_count index edbfb392e81..6f673eb98e6 100755 --- a/target/docker/mapping/cellranger_count/cellranger_count +++ b/target/docker/mapping/cellranger_count/cellranger_count @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# cellranger_count 1.0.1 +# cellranger_count 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -175,7 +175,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "cellranger_count 1.0.1" + echo "cellranger_count 1.0.2" echo "" echo "Align fastq files using Cell Ranger count." echo "" @@ -468,10 +468,10 @@ apt upgrade -y && apt install -y procps && rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Samuel D'Souza, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component mapping cellranger_count" -LABEL org.opencontainers.image.created="2024-06-18T14:14:55Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:11Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -626,7 +626,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "cellranger_count 1.0.1" + echo "cellranger_count 1.0.2" exit ;; --input) diff --git a/target/docker/mapping/cellranger_count_split/.config.vsh.yaml b/target/docker/mapping/cellranger_count_split/.config.vsh.yaml index b90b84d752e..d8f078e1c26 100644 --- a/target/docker/mapping/cellranger_count_split/.config.vsh.yaml +++ b/target/docker/mapping/cellranger_count_split/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "cellranger_count_split" namespace: "mapping" - version: "1.0.1" + version: "1.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -222,6 +222,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/cellranger_count_split" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/cellranger_count_split/cellranger_count_split" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/mapping/cellranger_count_split/cellranger_count_split b/target/docker/mapping/cellranger_count_split/cellranger_count_split index a980875d3db..999dbd2a83d 100755 --- a/target/docker/mapping/cellranger_count_split/cellranger_count_split +++ b/target/docker/mapping/cellranger_count_split/cellranger_count_split @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# cellranger_count_split 1.0.1 +# cellranger_count_split 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -175,7 +175,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "cellranger_count_split 1.0.1" + echo "cellranger_count_split 1.0.2" echo "" echo "Split 10x Cell Ranger output directory into separate output fields." echo "" @@ -433,10 +433,10 @@ ENTRYPOINT [] RUN apt update && apt upgrade -y LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Samuel D'Souza, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component mapping cellranger_count_split" -LABEL org.opencontainers.image.created="2024-06-18T14:14:59Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:11Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -591,7 +591,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "cellranger_count_split 1.0.1" + echo "cellranger_count_split 1.0.2" exit ;; --input) diff --git a/target/docker/mapping/cellranger_multi/.config.vsh.yaml b/target/docker/mapping/cellranger_multi/.config.vsh.yaml index 91805859b20..348fcd90faf 100644 --- a/target/docker/mapping/cellranger_multi/.config.vsh.yaml +++ b/target/docker/mapping/cellranger_multi/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "cellranger_multi" namespace: "mapping" - version: "1.0.1" + version: "1.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -585,6 +585,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/cellranger_multi" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/cellranger_multi/cellranger_multi" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/mapping/cellranger_multi/cellranger_multi b/target/docker/mapping/cellranger_multi/cellranger_multi index f376bae3c72..e3bbf14eec9 100755 --- a/target/docker/mapping/cellranger_multi/cellranger_multi +++ b/target/docker/mapping/cellranger_multi/cellranger_multi @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# cellranger_multi 1.0.1 +# cellranger_multi 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -175,7 +175,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "cellranger_multi 1.0.1" + echo "cellranger_multi 1.0.2" echo "" echo "Align fastq files using Cell Ranger multi." echo "" @@ -635,10 +635,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt, Dries De Maeyer" LABEL org.opencontainers.image.description="Companion container for running component mapping cellranger_multi" -LABEL org.opencontainers.image.created="2024-06-18T14:14:55Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:10Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -793,7 +793,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "cellranger_multi 1.0.1" + echo "cellranger_multi 1.0.2" exit ;; --input) diff --git a/target/docker/mapping/htseq_count/.config.vsh.yaml b/target/docker/mapping/htseq_count/.config.vsh.yaml index 4c1750f67c4..f1508279f24 100644 --- a/target/docker/mapping/htseq_count/.config.vsh.yaml +++ b/target/docker/mapping/htseq_count/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "htseq_count" namespace: "mapping" - version: "1.0.1" + version: "1.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -421,6 +421,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/htseq_count" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/htseq_count/htseq_count" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/mapping/htseq_count/htseq_count b/target/docker/mapping/htseq_count/htseq_count index af9be2e4e54..8dc61dd342f 100755 --- a/target/docker/mapping/htseq_count/htseq_count +++ b/target/docker/mapping/htseq_count/htseq_count @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# htseq_count 1.0.1 +# htseq_count 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "htseq_count 1.0.1" + echo "htseq_count 1.0.2" echo "" echo "Quantify gene expression for subsequent testing for differential expression." echo "" @@ -541,10 +541,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Angela Oliveira Pisco" LABEL org.opencontainers.image.description="Companion container for running component mapping htseq_count" -LABEL org.opencontainers.image.created="2024-06-18T14:14:58Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:11Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -699,7 +699,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "htseq_count 1.0.1" + echo "htseq_count 1.0.2" exit ;; --input) diff --git a/target/docker/mapping/htseq_count_to_h5mu/.config.vsh.yaml b/target/docker/mapping/htseq_count_to_h5mu/.config.vsh.yaml index 5649adfccdf..52d29d95af0 100644 --- a/target/docker/mapping/htseq_count_to_h5mu/.config.vsh.yaml +++ b/target/docker/mapping/htseq_count_to_h5mu/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "htseq_count_to_h5mu" namespace: "mapping" - version: "1.0.1" + version: "1.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -213,6 +213,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/htseq_count_to_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/htseq_count_to_h5mu/htseq_count_to_h5mu" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/mapping/htseq_count_to_h5mu/htseq_count_to_h5mu b/target/docker/mapping/htseq_count_to_h5mu/htseq_count_to_h5mu index 8090bd0e395..f3381a33d04 100755 --- a/target/docker/mapping/htseq_count_to_h5mu/htseq_count_to_h5mu +++ b/target/docker/mapping/htseq_count_to_h5mu/htseq_count_to_h5mu @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# htseq_count_to_h5mu 1.0.1 +# htseq_count_to_h5mu 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "htseq_count_to_h5mu 1.0.1" + echo "htseq_count_to_h5mu 1.0.2" echo "" echo "Convert the htseq table to a h5mu." echo "" @@ -436,10 +436,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Angela Oliveira Pisco" LABEL org.opencontainers.image.description="Companion container for running component mapping htseq_count_to_h5mu" -LABEL org.opencontainers.image.created="2024-06-18T14:14:56Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:12Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -594,7 +594,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "htseq_count_to_h5mu 1.0.1" + echo "htseq_count_to_h5mu 1.0.2" exit ;; --input_id) diff --git a/target/docker/mapping/multi_star/.config.vsh.yaml b/target/docker/mapping/multi_star/.config.vsh.yaml index 060d64228ad..ed60c7988cf 100644 --- a/target/docker/mapping/multi_star/.config.vsh.yaml +++ b/target/docker/mapping/multi_star/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "multi_star" namespace: "mapping" - version: "1.0.1" + version: "1.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -3083,6 +3083,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/multi_star" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/multi_star/multi_star" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/mapping/multi_star/multi_star b/target/docker/mapping/multi_star/multi_star index a7baff335dd..9aa3d391210 100755 --- a/target/docker/mapping/multi_star/multi_star +++ b/target/docker/mapping/multi_star/multi_star @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# multi_star 1.0.1 +# multi_star 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "multi_star 1.0.1" + echo "multi_star 1.0.2" echo "" echo "Align fastq files using STAR." echo "" @@ -1876,10 +1876,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component mapping multi_star" -LABEL org.opencontainers.image.created="2024-06-18T14:14:58Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:12Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -2034,7 +2034,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "multi_star 1.0.1" + echo "multi_star 1.0.2" exit ;; --input_id) diff --git a/target/docker/mapping/multi_star_to_h5mu/.config.vsh.yaml b/target/docker/mapping/multi_star_to_h5mu/.config.vsh.yaml index d346efe3350..b78b0d0d204 100644 --- a/target/docker/mapping/multi_star_to_h5mu/.config.vsh.yaml +++ b/target/docker/mapping/multi_star_to_h5mu/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "multi_star_to_h5mu" namespace: "mapping" - version: "1.0.1" + version: "1.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -183,6 +183,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/multi_star_to_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/multi_star_to_h5mu/multi_star_to_h5mu" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/mapping/multi_star_to_h5mu/multi_star_to_h5mu b/target/docker/mapping/multi_star_to_h5mu/multi_star_to_h5mu index a8185626310..38fb63c7218 100755 --- a/target/docker/mapping/multi_star_to_h5mu/multi_star_to_h5mu +++ b/target/docker/mapping/multi_star_to_h5mu/multi_star_to_h5mu @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# multi_star_to_h5mu 1.0.1 +# multi_star_to_h5mu 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "multi_star_to_h5mu 1.0.1" + echo "multi_star_to_h5mu 1.0.2" echo "" echo "Convert the output of \`multi_star\` to a h5mu." echo "" @@ -425,10 +425,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Angela Oliveira Pisco" LABEL org.opencontainers.image.description="Companion container for running component mapping multi_star_to_h5mu" -LABEL org.opencontainers.image.created="2024-06-18T14:14:56Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:10Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -583,7 +583,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "multi_star_to_h5mu 1.0.1" + echo "multi_star_to_h5mu 1.0.2" exit ;; --input) diff --git a/target/docker/mapping/samtools_sort/.config.vsh.yaml b/target/docker/mapping/samtools_sort/.config.vsh.yaml index f1488e5b35a..ae33a0d26e4 100644 --- a/target/docker/mapping/samtools_sort/.config.vsh.yaml +++ b/target/docker/mapping/samtools_sort/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "samtools_sort" namespace: "mapping" - version: "1.0.1" + version: "1.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -273,6 +273,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/samtools_sort" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/samtools_sort/samtools_sort" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/mapping/samtools_sort/samtools_sort b/target/docker/mapping/samtools_sort/samtools_sort index dcd87647ecb..bd266222491 100755 --- a/target/docker/mapping/samtools_sort/samtools_sort +++ b/target/docker/mapping/samtools_sort/samtools_sort @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# samtools_sort 1.0.1 +# samtools_sort 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "samtools_sort 1.0.1" + echo "samtools_sort 1.0.2" echo "" echo "Sort and (optionally) index alignments." echo "" @@ -481,10 +481,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Angela Oliveira Pisco" LABEL org.opencontainers.image.description="Companion container for running component mapping samtools_sort" -LABEL org.opencontainers.image.created="2024-06-18T14:14:59Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:10Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -639,7 +639,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "samtools_sort 1.0.1" + echo "samtools_sort 1.0.2" exit ;; --input) diff --git a/target/docker/mapping/star_align/.config.vsh.yaml b/target/docker/mapping/star_align/.config.vsh.yaml index 664e12e92b8..0a3122814c8 100644 --- a/target/docker/mapping/star_align/.config.vsh.yaml +++ b/target/docker/mapping/star_align/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "star_align" namespace: "mapping" - version: "1.0.1" + version: "1.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -2538,6 +2538,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/star_align" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/star_align/star_align" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/mapping/star_align/star_align b/target/docker/mapping/star_align/star_align index a3b184a538b..5efa45678ef 100755 --- a/target/docker/mapping/star_align/star_align +++ b/target/docker/mapping/star_align/star_align @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# star_align 1.0.1 +# star_align 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "star_align 1.0.1" + echo "star_align 1.0.2" echo "" echo "Align fastq files using STAR." echo "" @@ -1804,10 +1804,10 @@ RUN apt-get update && \ LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component mapping star_align" -LABEL org.opencontainers.image.created="2024-06-18T14:14:56Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:11Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -1962,7 +1962,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "star_align 1.0.1" + echo "star_align 1.0.2" exit ;; --input) diff --git a/target/docker/mapping/star_align_v273a/.config.vsh.yaml b/target/docker/mapping/star_align_v273a/.config.vsh.yaml index 63c1e23158f..50236f65415 100644 --- a/target/docker/mapping/star_align_v273a/.config.vsh.yaml +++ b/target/docker/mapping/star_align_v273a/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "star_align_v273a" namespace: "mapping" - version: "1.0.1" + version: "1.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -2538,6 +2538,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/star_align_v273a" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/star_align_v273a/star_align_v273a" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/mapping/star_align_v273a/star_align_v273a b/target/docker/mapping/star_align_v273a/star_align_v273a index 09b90a56c10..204cb47db3d 100755 --- a/target/docker/mapping/star_align_v273a/star_align_v273a +++ b/target/docker/mapping/star_align_v273a/star_align_v273a @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# star_align_v273a 1.0.1 +# star_align_v273a 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "star_align_v273a 1.0.1" + echo "star_align_v273a 1.0.2" echo "" echo "Align fastq files using STAR." echo "" @@ -1804,10 +1804,10 @@ RUN apt-get update && \ LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component mapping star_align_v273a" -LABEL org.opencontainers.image.created="2024-06-18T14:14:54Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:12Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -1962,7 +1962,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "star_align_v273a 1.0.1" + echo "star_align_v273a 1.0.2" exit ;; --input) diff --git a/target/docker/mapping/star_build_reference/.config.vsh.yaml b/target/docker/mapping/star_build_reference/.config.vsh.yaml index dca7950555d..e5531664a96 100644 --- a/target/docker/mapping/star_build_reference/.config.vsh.yaml +++ b/target/docker/mapping/star_build_reference/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "star_build_reference" namespace: "mapping" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -193,6 +193,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/star_build_reference" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/mapping/star_build_reference/star_build_reference" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/mapping/star_build_reference/star_build_reference b/target/docker/mapping/star_build_reference/star_build_reference index 4e50ea9d208..f375384118c 100755 --- a/target/docker/mapping/star_build_reference/star_build_reference +++ b/target/docker/mapping/star_build_reference/star_build_reference @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# star_build_reference 1.0.1 +# star_build_reference 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "star_build_reference 1.0.1" + echo "star_build_reference 1.0.2" echo "" echo "Create a reference for STAR from a set of fasta files." echo "" @@ -452,10 +452,10 @@ RUN apt-get update && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component mapping star_build_reference" -LABEL org.opencontainers.image.created="2024-06-18T14:14:58Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:10Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -610,7 +610,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "star_build_reference 1.0.1" + echo "star_build_reference 1.0.2" exit ;; --genome_fasta) diff --git a/target/docker/metadata/add_id/.config.vsh.yaml b/target/docker/metadata/add_id/.config.vsh.yaml index 9744cb5019c..144d030dc62 100644 --- a/target/docker/metadata/add_id/.config.vsh.yaml +++ b/target/docker/metadata/add_id/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "add_id" namespace: "metadata" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -209,6 +209,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/metadata/add_id" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/metadata/add_id/add_id" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/metadata/add_id/add_id b/target/docker/metadata/add_id/add_id index 96825d8f101..ee5a9aa51a7 100755 --- a/target/docker/metadata/add_id/add_id +++ b/target/docker/metadata/add_id/add_id @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# add_id 1.0.1 +# add_id 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "add_id 1.0.1" + echo "add_id 1.0.2" echo "" echo "Add id of .obs. Also allows to make .obs_names (the .obs index) unique" echo "by prefixing the values with an unique id per .h5mu file." @@ -437,10 +437,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component metadata add_id" -LABEL org.opencontainers.image.created="2024-06-18T14:14:57Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:11Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -595,7 +595,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "add_id 1.0.1" + echo "add_id 1.0.2" exit ;; --input) diff --git a/target/docker/metadata/grep_annotation_column/.config.vsh.yaml b/target/docker/metadata/grep_annotation_column/.config.vsh.yaml index 0f0faf96a7c..14235b906af 100644 --- a/target/docker/metadata/grep_annotation_column/.config.vsh.yaml +++ b/target/docker/metadata/grep_annotation_column/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "grep_annotation_column" namespace: "metadata" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -267,6 +267,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/metadata/grep_annotation_column" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/metadata/grep_annotation_column/grep_annotation_column" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/metadata/grep_annotation_column/grep_annotation_column b/target/docker/metadata/grep_annotation_column/grep_annotation_column index d0fc9f9e7bc..0e66e5e4517 100755 --- a/target/docker/metadata/grep_annotation_column/grep_annotation_column +++ b/target/docker/metadata/grep_annotation_column/grep_annotation_column @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# grep_annotation_column 1.0.1 +# grep_annotation_column 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "grep_annotation_column 1.0.1" + echo "grep_annotation_column 1.0.2" echo "" echo "Perform a regex lookup on a column from the annotation matrices .obs or .var." echo "The annotation matrix can originate from either a modality, or all modalities" @@ -470,10 +470,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component metadata grep_annotation_column" -LABEL org.opencontainers.image.created="2024-06-18T14:14:57Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:12Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -628,7 +628,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "grep_annotation_column 1.0.1" + echo "grep_annotation_column 1.0.2" exit ;; --input) diff --git a/target/docker/metadata/join_csv/.config.vsh.yaml b/target/docker/metadata/join_csv/.config.vsh.yaml index 90ad65b0e7c..9ef0576d258 100644 --- a/target/docker/metadata/join_csv/.config.vsh.yaml +++ b/target/docker/metadata/join_csv/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "join_csv" namespace: "metadata" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -241,6 +241,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/metadata/join_csv" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/metadata/join_csv/join_csv" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/metadata/join_csv/join_csv b/target/docker/metadata/join_csv/join_csv index 137cdab662d..308c96f7ef6 100755 --- a/target/docker/metadata/join_csv/join_csv +++ b/target/docker/metadata/join_csv/join_csv @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# join_csv 1.0.1 +# join_csv 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "join_csv 1.0.1" + echo "join_csv 1.0.2" echo "" echo "Join a csv containing metadata to the .obs or .var field of a mudata file." echo "" @@ -453,10 +453,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component metadata join_csv" -LABEL org.opencontainers.image.created="2024-06-18T14:14:57Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:11Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -611,7 +611,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "join_csv 1.0.1" + echo "join_csv 1.0.2" exit ;; --input) diff --git a/target/docker/metadata/join_uns_to_obs/.config.vsh.yaml b/target/docker/metadata/join_uns_to_obs/.config.vsh.yaml index e64b5479077..8ac4df0e127 100644 --- a/target/docker/metadata/join_uns_to_obs/.config.vsh.yaml +++ b/target/docker/metadata/join_uns_to_obs/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "join_uns_to_obs" namespace: "metadata" - version: "1.0.1" + version: "1.0.2" arguments: - type: "file" name: "--input" @@ -183,6 +183,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/metadata/join_uns_to_obs" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/metadata/join_uns_to_obs/join_uns_to_obs" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/metadata/join_uns_to_obs/join_uns_to_obs b/target/docker/metadata/join_uns_to_obs/join_uns_to_obs index 284187ac0c1..b21efb01af8 100755 --- a/target/docker/metadata/join_uns_to_obs/join_uns_to_obs +++ b/target/docker/metadata/join_uns_to_obs/join_uns_to_obs @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# join_uns_to_obs 1.0.1 +# join_uns_to_obs 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -170,7 +170,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "join_uns_to_obs 1.0.1" + echo "join_uns_to_obs 1.0.2" echo "" echo "Join a data frame of length 1 (1 row index value) in .uns containing metadata to" echo "the .obs of a mudata file." @@ -428,10 +428,10 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "anndata~=0.9.1" "mudata~=0.2.3" "pandas!=2.1.2" LABEL org.opencontainers.image.description="Companion container for running component metadata join_uns_to_obs" -LABEL org.opencontainers.image.created="2024-06-18T14:14:58Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:11Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -586,7 +586,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "join_uns_to_obs 1.0.1" + echo "join_uns_to_obs 1.0.2" exit ;; --input) diff --git a/target/docker/metadata/move_obsm_to_obs/.config.vsh.yaml b/target/docker/metadata/move_obsm_to_obs/.config.vsh.yaml index 23a48004dc5..6ad8a019e33 100644 --- a/target/docker/metadata/move_obsm_to_obs/.config.vsh.yaml +++ b/target/docker/metadata/move_obsm_to_obs/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "move_obsm_to_obs" namespace: "metadata" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -204,6 +204,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/metadata/move_obsm_to_obs" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/metadata/move_obsm_to_obs/move_obsm_to_obs" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/metadata/move_obsm_to_obs/move_obsm_to_obs b/target/docker/metadata/move_obsm_to_obs/move_obsm_to_obs index 725bfbada74..ecdfa564c80 100755 --- a/target/docker/metadata/move_obsm_to_obs/move_obsm_to_obs +++ b/target/docker/metadata/move_obsm_to_obs/move_obsm_to_obs @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# move_obsm_to_obs 1.0.1 +# move_obsm_to_obs 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "move_obsm_to_obs 1.0.1" + echo "move_obsm_to_obs 1.0.2" echo "" echo "Move a matrix from .obsm to .obs. Newly created columns in .obs will" echo "be created from the .obsm key suffixed with an underscore and the name of the" @@ -436,10 +436,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component metadata move_obsm_to_obs" -LABEL org.opencontainers.image.created="2024-06-18T14:14:58Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:11Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -594,7 +594,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "move_obsm_to_obs 1.0.1" + echo "move_obsm_to_obs 1.0.2" exit ;; --input) diff --git a/target/docker/neighbors/bbknn/.config.vsh.yaml b/target/docker/neighbors/bbknn/.config.vsh.yaml index 905502b3d87..243606c422f 100644 --- a/target/docker/neighbors/bbknn/.config.vsh.yaml +++ b/target/docker/neighbors/bbknn/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "bbknn" namespace: "neighbors" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries De Maeyer" roles: @@ -294,6 +294,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/neighbors/bbknn" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/neighbors/bbknn/bbknn" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/neighbors/bbknn/bbknn b/target/docker/neighbors/bbknn/bbknn index 022dedb92cf..c037a538506 100755 --- a/target/docker/neighbors/bbknn/bbknn +++ b/target/docker/neighbors/bbknn/bbknn @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# bbknn 1.0.1 +# bbknn 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "bbknn 1.0.1" + echo "bbknn 1.0.2" echo "" echo "BBKNN network generation" echo "" @@ -478,10 +478,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries De Maeyer, Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component neighbors bbknn" -LABEL org.opencontainers.image.created="2024-06-18T14:14:59Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:10Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -636,7 +636,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bbknn 1.0.1" + echo "bbknn 1.0.2" exit ;; --input) diff --git a/target/docker/neighbors/find_neighbors/.config.vsh.yaml b/target/docker/neighbors/find_neighbors/.config.vsh.yaml index f4c54632cdc..7eb84f75cd5 100644 --- a/target/docker/neighbors/find_neighbors/.config.vsh.yaml +++ b/target/docker/neighbors/find_neighbors/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "find_neighbors" namespace: "neighbors" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries De Maeyer" roles: @@ -314,6 +314,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/neighbors/find_neighbors" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/neighbors/find_neighbors/find_neighbors" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/neighbors/find_neighbors/find_neighbors b/target/docker/neighbors/find_neighbors/find_neighbors index 9c89fd3b7cc..534382dcb6f 100755 --- a/target/docker/neighbors/find_neighbors/find_neighbors +++ b/target/docker/neighbors/find_neighbors/find_neighbors @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# find_neighbors 1.0.1 +# find_neighbors 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "find_neighbors 1.0.1" + echo "find_neighbors 1.0.2" echo "" echo "Compute a neighborhood graph of observations [McInnes18]." echo "" @@ -483,10 +483,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries De Maeyer, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component neighbors find_neighbors" -LABEL org.opencontainers.image.created="2024-06-18T14:14:59Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:10Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "find_neighbors 1.0.1" + echo "find_neighbors 1.0.2" exit ;; --input) diff --git a/target/docker/process_10xh5/filter_10xh5/.config.vsh.yaml b/target/docker/process_10xh5/filter_10xh5/.config.vsh.yaml index 29446d988a1..683d35b3c5c 100644 --- a/target/docker/process_10xh5/filter_10xh5/.config.vsh.yaml +++ b/target/docker/process_10xh5/filter_10xh5/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "filter_10xh5" namespace: "process_10xh5" - version: "1.0.1" + version: "1.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -200,6 +200,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/process_10xh5/filter_10xh5" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/process_10xh5/filter_10xh5/filter_10xh5" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/process_10xh5/filter_10xh5/filter_10xh5 b/target/docker/process_10xh5/filter_10xh5/filter_10xh5 index c65454ec853..e01083930c2 100755 --- a/target/docker/process_10xh5/filter_10xh5/filter_10xh5 +++ b/target/docker/process_10xh5/filter_10xh5/filter_10xh5 @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# filter_10xh5 1.0.1 +# filter_10xh5 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "filter_10xh5 1.0.1" + echo "filter_10xh5 1.0.2" echo "" echo "Filter a 10x h5 dataset." echo "" @@ -446,10 +446,10 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component process_10xh5 filter_10xh5" -LABEL org.opencontainers.image.created="2024-06-18T14:14:56Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:09Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -604,7 +604,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "filter_10xh5 1.0.1" + echo "filter_10xh5 1.0.2" exit ;; --input) diff --git a/target/docker/qc/calculate_qc_metrics/.config.vsh.yaml b/target/docker/qc/calculate_qc_metrics/.config.vsh.yaml index c024cb6b4f5..50cca9ca979 100644 --- a/target/docker/qc/calculate_qc_metrics/.config.vsh.yaml +++ b/target/docker/qc/calculate_qc_metrics/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "calculate_qc_metrics" namespace: "qc" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -320,6 +320,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/qc/calculate_qc_metrics" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/qc/calculate_qc_metrics/calculate_qc_metrics" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/qc/calculate_qc_metrics/calculate_qc_metrics b/target/docker/qc/calculate_qc_metrics/calculate_qc_metrics index ae7670e6b81..eaddd5bca97 100755 --- a/target/docker/qc/calculate_qc_metrics/calculate_qc_metrics +++ b/target/docker/qc/calculate_qc_metrics/calculate_qc_metrics @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# calculate_qc_metrics 1.0.1 +# calculate_qc_metrics 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "calculate_qc_metrics 1.0.1" + echo "calculate_qc_metrics 1.0.2" echo "" echo "Add basic quality control metrics to an .h5mu file." echo "" @@ -516,10 +516,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component qc calculate_qc_metrics" -LABEL org.opencontainers.image.created="2024-06-18T14:14:58Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:07Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -674,7 +674,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "calculate_qc_metrics 1.0.1" + echo "calculate_qc_metrics 1.0.2" exit ;; --input) diff --git a/target/docker/qc/fastqc/.config.vsh.yaml b/target/docker/qc/fastqc/.config.vsh.yaml index 9cdd34723e5..82d84f147d5 100644 --- a/target/docker/qc/fastqc/.config.vsh.yaml +++ b/target/docker/qc/fastqc/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "fastqc" namespace: "qc" - version: "1.0.1" + version: "1.0.2" arguments: - type: "string" name: "--mode" @@ -159,6 +159,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/qc/fastqc" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/qc/fastqc/fastqc" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/qc/fastqc/fastqc b/target/docker/qc/fastqc/fastqc index 5edb7f4a5ba..c6ee68a7553 100755 --- a/target/docker/qc/fastqc/fastqc +++ b/target/docker/qc/fastqc/fastqc @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# fastqc 1.0.1 +# fastqc 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -170,7 +170,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "fastqc 1.0.1" + echo "fastqc 1.0.2" echo "" echo "Fastqc component, please see" echo "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. This component can" @@ -425,10 +425,10 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component qc fastqc" -LABEL org.opencontainers.image.created="2024-06-18T14:14:58Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:07Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -583,7 +583,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "fastqc 1.0.1" + echo "fastqc 1.0.2" exit ;; --mode) diff --git a/target/docker/qc/multiqc/.config.vsh.yaml b/target/docker/qc/multiqc/.config.vsh.yaml index 52ad19c8239..8cbcacdb66f 100644 --- a/target/docker/qc/multiqc/.config.vsh.yaml +++ b/target/docker/qc/multiqc/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "multiqc" namespace: "qc" - version: "1.0.1" + version: "1.0.2" arguments: - type: "file" name: "--input" @@ -143,6 +143,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/qc/multiqc" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/qc/multiqc/multiqc" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/qc/multiqc/multiqc b/target/docker/qc/multiqc/multiqc index 30207724526..23df62114c7 100755 --- a/target/docker/qc/multiqc/multiqc +++ b/target/docker/qc/multiqc/multiqc @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# multiqc 1.0.1 +# multiqc 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -170,7 +170,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "multiqc 1.0.1" + echo "multiqc 1.0.2" echo "" echo "MultiQC aggregates results from bioinformatics analyses across many samples into" echo "a single report." @@ -418,10 +418,10 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "multiqc" LABEL org.opencontainers.image.description="Companion container for running component qc multiqc" -LABEL org.opencontainers.image.created="2024-06-18T14:14:58Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:07Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -576,7 +576,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "multiqc 1.0.1" + echo "multiqc 1.0.2" exit ;; --input) diff --git a/target/docker/query/cellxgene_census/.config.vsh.yaml b/target/docker/query/cellxgene_census/.config.vsh.yaml index 2096e63f853..264af58a67e 100644 --- a/target/docker/query/cellxgene_census/.config.vsh.yaml +++ b/target/docker/query/cellxgene_census/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "cellxgene_census" namespace: "query" - version: "1.0.1" + version: "1.0.2" authors: - name: "Matthias Beyens" roles: @@ -519,6 +519,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/query/cellxgene_census" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/query/cellxgene_census/cellxgene_census" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/query/cellxgene_census/cellxgene_census b/target/docker/query/cellxgene_census/cellxgene_census index 5b9aebcd5b6..f63fa8b9680 100755 --- a/target/docker/query/cellxgene_census/cellxgene_census +++ b/target/docker/query/cellxgene_census/cellxgene_census @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# cellxgene_census 1.0.1 +# cellxgene_census 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -176,7 +176,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "cellxgene_census 1.0.1" + echo "cellxgene_census 1.0.2" echo "" echo "Query cells from a CellxGene Census or custom TileDBSoma object." echo "Aside from fetching the cells' RNA counts (\`.X\`), cell metadata" @@ -507,10 +507,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Matthias Beyens, Dries De Maeyer, Robrecht Cannoodt, Kai Waldrant" LABEL org.opencontainers.image.description="Companion container for running component query cellxgene_census" -LABEL org.opencontainers.image.created="2024-06-18T14:14:59Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:09Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -665,7 +665,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "cellxgene_census 1.0.1" + echo "cellxgene_census 1.0.2" exit ;; --input_uri) diff --git a/target/docker/reference/build_bdrhap_reference/.config.vsh.yaml b/target/docker/reference/build_bdrhap_reference/.config.vsh.yaml index e0ed4827dda..b72c7cbed5e 100644 --- a/target/docker/reference/build_bdrhap_reference/.config.vsh.yaml +++ b/target/docker/reference/build_bdrhap_reference/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "build_bdrhap_reference" namespace: "reference" - version: "1.0.1" + version: "1.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -188,6 +188,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/reference/build_bdrhap_reference" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/reference/build_bdrhap_reference/build_bdrhap_reference" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/reference/build_bdrhap_reference/build_bdrhap_reference b/target/docker/reference/build_bdrhap_reference/build_bdrhap_reference index 2be81b04e80..8731d6e3cc3 100755 --- a/target/docker/reference/build_bdrhap_reference/build_bdrhap_reference +++ b/target/docker/reference/build_bdrhap_reference/build_bdrhap_reference @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# build_bdrhap_reference 1.0.1 +# build_bdrhap_reference 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "build_bdrhap_reference 1.0.1" + echo "build_bdrhap_reference 1.0.2" echo "" echo "Compile a reference into a STAR index compatible with the BD Rhapsody pipeline." echo "" @@ -421,10 +421,10 @@ RUN apt-get update && \ LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component reference build_bdrhap_reference" -LABEL org.opencontainers.image.created="2024-06-18T14:14:55Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:09Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -579,7 +579,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "build_bdrhap_reference 1.0.1" + echo "build_bdrhap_reference 1.0.2" exit ;; --genome_fasta) diff --git a/target/docker/reference/build_cellranger_reference/.config.vsh.yaml b/target/docker/reference/build_cellranger_reference/.config.vsh.yaml index 3b09938bdea..49075f53c7d 100644 --- a/target/docker/reference/build_cellranger_reference/.config.vsh.yaml +++ b/target/docker/reference/build_cellranger_reference/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "build_cellranger_reference" namespace: "reference" - version: "1.0.1" + version: "1.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -188,6 +188,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/reference/build_cellranger_reference" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/reference/build_cellranger_reference/build_cellranger_reference" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/reference/build_cellranger_reference/build_cellranger_reference b/target/docker/reference/build_cellranger_reference/build_cellranger_reference index 99c044d0f4e..04dfb24d306 100755 --- a/target/docker/reference/build_cellranger_reference/build_cellranger_reference +++ b/target/docker/reference/build_cellranger_reference/build_cellranger_reference @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# build_cellranger_reference 1.0.1 +# build_cellranger_reference 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "build_cellranger_reference 1.0.1" + echo "build_cellranger_reference 1.0.2" echo "" echo "Build a Cell Ranger-compatible reference folder from user-supplied genome FASTA" echo "and gene GTF files. Creates a new folder named after the genome." @@ -421,10 +421,10 @@ apt upgrade -y && apt install -y procps pigz && rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component reference build_cellranger_reference" -LABEL org.opencontainers.image.created="2024-06-18T14:14:55Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:08Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -579,7 +579,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "build_cellranger_reference 1.0.1" + echo "build_cellranger_reference 1.0.2" exit ;; --genome_fasta) diff --git a/target/docker/reference/make_reference/.config.vsh.yaml b/target/docker/reference/make_reference/.config.vsh.yaml index ee6be3c7033..6a79938c0bc 100644 --- a/target/docker/reference/make_reference/.config.vsh.yaml +++ b/target/docker/reference/make_reference/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "make_reference" namespace: "reference" - version: "1.0.1" + version: "1.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -215,6 +215,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/reference/make_reference" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/reference/make_reference/make_reference" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/reference/make_reference/make_reference b/target/docker/reference/make_reference/make_reference index 1c48b0cd322..728613529d5 100755 --- a/target/docker/reference/make_reference/make_reference +++ b/target/docker/reference/make_reference/make_reference @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# make_reference 1.0.1 +# make_reference 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "make_reference 1.0.1" + echo "make_reference 1.0.2" echo "" echo "Preprocess and build a transcriptome reference." echo "" @@ -443,10 +443,10 @@ RUN apt-get update && \ LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component reference make_reference" -LABEL org.opencontainers.image.created="2024-06-18T14:14:54Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:09Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -601,7 +601,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "make_reference 1.0.1" + echo "make_reference 1.0.2" exit ;; --genome_fasta) diff --git a/target/docker/report/mermaid/.config.vsh.yaml b/target/docker/report/mermaid/.config.vsh.yaml index f0b977caf27..9a37102f149 100644 --- a/target/docker/report/mermaid/.config.vsh.yaml +++ b/target/docker/report/mermaid/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "mermaid" namespace: "report" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries De Maeyer" roles: @@ -188,6 +188,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/report/mermaid" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/report/mermaid/mermaid" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/report/mermaid/mermaid b/target/docker/report/mermaid/mermaid index e35063368e0..22b4ce0d832 100755 --- a/target/docker/report/mermaid/mermaid +++ b/target/docker/report/mermaid/mermaid @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# mermaid 1.0.1 +# mermaid 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "mermaid 1.0.1" + echo "mermaid 1.0.2" echo "" echo "Generates a network from mermaid code." echo "" @@ -438,10 +438,10 @@ RUN apt-get update && \ LABEL org.opencontainers.image.authors="Dries De Maeyer" LABEL org.opencontainers.image.description="Companion container for running component report mermaid" -LABEL org.opencontainers.image.created="2024-06-18T14:15:01Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:08Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -596,7 +596,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "mermaid 1.0.1" + echo "mermaid 1.0.2" exit ;; --input) diff --git a/target/docker/transfer/publish/.config.vsh.yaml b/target/docker/transfer/publish/.config.vsh.yaml index a3d3867b63c..3f0b6f8eb43 100644 --- a/target/docker/transfer/publish/.config.vsh.yaml +++ b/target/docker/transfer/publish/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "publish" namespace: "transfer" - version: "1.0.1" + version: "1.0.2" authors: - name: "Toni Verbeiren" roles: @@ -128,6 +128,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/transfer/publish" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/transfer/publish/publish" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/transfer/publish/publish b/target/docker/transfer/publish/publish index 49fe897e206..dbd46b22f09 100755 --- a/target/docker/transfer/publish/publish +++ b/target/docker/transfer/publish/publish @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# publish 1.0.1 +# publish 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "publish 1.0.1" + echo "publish 1.0.2" echo "" echo "Publish an artifact and optionally rename with parameters" echo "" @@ -410,10 +410,10 @@ ENTRYPOINT [] RUN : LABEL org.opencontainers.image.authors="Toni Verbeiren" LABEL org.opencontainers.image.description="Companion container for running component transfer publish" -LABEL org.opencontainers.image.created="2024-06-18T14:14:54Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:06Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -568,7 +568,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "publish 1.0.1" + echo "publish 1.0.2" exit ;; --input) diff --git a/target/docker/transform/clr/.config.vsh.yaml b/target/docker/transform/clr/.config.vsh.yaml index fe73ffd404c..b243f3f09cd 100644 --- a/target/docker/transform/clr/.config.vsh.yaml +++ b/target/docker/transform/clr/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "clr" namespace: "transform" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -202,6 +202,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/transform/clr" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/transform/clr/clr" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/transform/clr/clr b/target/docker/transform/clr/clr index 73318e7461d..923193cd134 100755 --- a/target/docker/transform/clr/clr +++ b/target/docker/transform/clr/clr @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# clr 1.0.1 +# clr 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "clr 1.0.1" + echo "clr 1.0.2" echo "" echo "Perform CLR normalization on CITE-seq data (Stoeckius et al., 2017)." echo "" @@ -436,10 +436,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component transform clr" -LABEL org.opencontainers.image.created="2024-06-18T14:14:55Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:05Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -594,7 +594,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "clr 1.0.1" + echo "clr 1.0.2" exit ;; --input) diff --git a/target/docker/transform/delete_layer/.config.vsh.yaml b/target/docker/transform/delete_layer/.config.vsh.yaml index b8bb3c87ab6..0d60efb3136 100644 --- a/target/docker/transform/delete_layer/.config.vsh.yaml +++ b/target/docker/transform/delete_layer/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "delete_layer" namespace: "transform" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -200,6 +200,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/transform/delete_layer" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/transform/delete_layer/delete_layer" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/transform/delete_layer/delete_layer b/target/docker/transform/delete_layer/delete_layer index f180e91a260..a2e33f1e05b 100755 --- a/target/docker/transform/delete_layer/delete_layer +++ b/target/docker/transform/delete_layer/delete_layer @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# delete_layer 1.0.1 +# delete_layer 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "delete_layer 1.0.1" + echo "delete_layer 1.0.2" echo "" echo "Delete an anndata layer from one or more modalities." echo "" @@ -436,10 +436,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component transform delete_layer" -LABEL org.opencontainers.image.created="2024-06-18T14:14:55Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:06Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -594,7 +594,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "delete_layer 1.0.1" + echo "delete_layer 1.0.2" exit ;; --input) diff --git a/target/docker/transform/log1p/.config.vsh.yaml b/target/docker/transform/log1p/.config.vsh.yaml index 339781c210a..476bae765dc 100644 --- a/target/docker/transform/log1p/.config.vsh.yaml +++ b/target/docker/transform/log1p/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "log1p" namespace: "transform" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries De Maeyer" roles: @@ -230,6 +230,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/transform/log1p" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/transform/log1p/log1p" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/transform/log1p/log1p b/target/docker/transform/log1p/log1p index 507ee65ea38..071e16830a3 100755 --- a/target/docker/transform/log1p/log1p +++ b/target/docker/transform/log1p/log1p @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# log1p 1.0.1 +# log1p 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "log1p 1.0.1" + echo "log1p 1.0.2" echo "" echo "Logarithmize the data matrix. Computes X = log(X + 1), where log denotes the" echo "natural logarithm unless a different base is given." @@ -442,10 +442,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries De Maeyer, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component transform log1p" -LABEL org.opencontainers.image.created="2024-06-18T14:14:55Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:05Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -600,7 +600,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "log1p 1.0.1" + echo "log1p 1.0.2" exit ;; --input) diff --git a/target/docker/transform/move_layer/.config.vsh.yaml b/target/docker/transform/move_layer/.config.vsh.yaml index 3eb59b94a83..92c54e398c2 100644 --- a/target/docker/transform/move_layer/.config.vsh.yaml +++ b/target/docker/transform/move_layer/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "move_layer" namespace: "transform" - version: "1.0.1" + version: "1.0.2" arguments: - type: "file" name: "--input" @@ -183,6 +183,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/transform/move_layer" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/transform/move_layer/move_layer" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/transform/move_layer/move_layer b/target/docker/transform/move_layer/move_layer index 04529b5c6f2..646e032b391 100755 --- a/target/docker/transform/move_layer/move_layer +++ b/target/docker/transform/move_layer/move_layer @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# move_layer 1.0.1 +# move_layer 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -170,7 +170,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "move_layer 1.0.1" + echo "move_layer 1.0.2" echo "" echo "Move a data matrix stored at the .layers or .X attributes in a MuData object to" echo "another layer." @@ -431,10 +431,10 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "anndata~=0.9.1" "mudata~=0.2.3" "pandas!=2.1.2" LABEL org.opencontainers.image.description="Companion container for running component transform move_layer" -LABEL org.opencontainers.image.created="2024-06-18T14:14:56Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:06Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -589,7 +589,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "move_layer 1.0.1" + echo "move_layer 1.0.2" exit ;; --input) diff --git a/target/docker/transform/normalize_total/.config.vsh.yaml b/target/docker/transform/normalize_total/.config.vsh.yaml index 6a388fe90c1..88a53e0f667 100644 --- a/target/docker/transform/normalize_total/.config.vsh.yaml +++ b/target/docker/transform/normalize_total/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "normalize_total" namespace: "transform" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries De Maeyer" roles: @@ -247,6 +247,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/transform/normalize_total" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/transform/normalize_total/normalize_total" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/transform/normalize_total/normalize_total b/target/docker/transform/normalize_total/normalize_total index d55fd80be9c..0cbbfcb9087 100755 --- a/target/docker/transform/normalize_total/normalize_total +++ b/target/docker/transform/normalize_total/normalize_total @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# normalize_total 1.0.1 +# normalize_total 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "normalize_total 1.0.1" + echo "normalize_total 1.0.2" echo "" echo "Normalize counts per cell." echo "" @@ -460,10 +460,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries De Maeyer, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component transform normalize_total" -LABEL org.opencontainers.image.created="2024-06-18T14:14:56Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:12Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -618,7 +618,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "normalize_total 1.0.1" + echo "normalize_total 1.0.2" exit ;; --input) diff --git a/target/docker/transform/regress_out/.config.vsh.yaml b/target/docker/transform/regress_out/.config.vsh.yaml index c6a90cbe46e..8a968f3f464 100644 --- a/target/docker/transform/regress_out/.config.vsh.yaml +++ b/target/docker/transform/regress_out/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "regress_out" namespace: "transform" - version: "1.0.1" + version: "1.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -200,6 +200,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/transform/regress_out" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/transform/regress_out/regress_out" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/transform/regress_out/regress_out b/target/docker/transform/regress_out/regress_out index 3cab789743b..622f8649505 100755 --- a/target/docker/transform/regress_out/regress_out +++ b/target/docker/transform/regress_out/regress_out @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# regress_out 1.0.1 +# regress_out 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "regress_out 1.0.1" + echo "regress_out 1.0.2" echo "" echo "Regress out (mostly) unwanted sources of variation." echo "Uses simple linear regression. This is inspired by Seurat's regressOut function" @@ -438,10 +438,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component transform regress_out" -LABEL org.opencontainers.image.created="2024-06-18T14:14:56Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:06Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -596,7 +596,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "regress_out 1.0.1" + echo "regress_out 1.0.2" exit ;; --input) diff --git a/target/docker/transform/scale/.config.vsh.yaml b/target/docker/transform/scale/.config.vsh.yaml index 1ddcb6f1f7c..f9e735dfe52 100644 --- a/target/docker/transform/scale/.config.vsh.yaml +++ b/target/docker/transform/scale/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "scale" namespace: "transform" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -210,6 +210,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/transform/scale" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/transform/scale/scale" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/transform/scale/scale b/target/docker/transform/scale/scale index 92ec09f1170..a319ccba3d3 100755 --- a/target/docker/transform/scale/scale +++ b/target/docker/transform/scale/scale @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# scale 1.0.1 +# scale 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "scale 1.0.1" + echo "scale 1.0.2" echo "" echo "Scale data to unit variance and zero mean." echo "" @@ -439,10 +439,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component transform scale" -LABEL org.opencontainers.image.created="2024-06-18T14:14:56Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:12Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -597,7 +597,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "scale 1.0.1" + echo "scale 1.0.2" exit ;; --input) diff --git a/target/docker/velocity/scvelo/.config.vsh.yaml b/target/docker/velocity/scvelo/.config.vsh.yaml index 17a901a7dcc..c15fff9f9ab 100644 --- a/target/docker/velocity/scvelo/.config.vsh.yaml +++ b/target/docker/velocity/scvelo/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "scvelo" namespace: "velocity" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -282,6 +282,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/velocity/scvelo" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/velocity/scvelo/scvelo" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/velocity/scvelo/scvelo b/target/docker/velocity/scvelo/scvelo index 60a2e4dd33b..aba7474404d 100755 --- a/target/docker/velocity/scvelo/scvelo +++ b/target/docker/velocity/scvelo/scvelo @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# scvelo 1.0.1 +# scvelo 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "scvelo 1.0.1" + echo "scvelo 1.0.2" echo "" echo "Inputs:" echo " --input" @@ -479,10 +479,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component velocity scvelo" -LABEL org.opencontainers.image.created="2024-06-18T14:15:00Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:06Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -637,7 +637,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "scvelo 1.0.1" + echo "scvelo 1.0.2" exit ;; --input) diff --git a/target/docker/velocity/velocyto/.config.vsh.yaml b/target/docker/velocity/velocyto/.config.vsh.yaml index b3126278d2b..5a3ce994365 100644 --- a/target/docker/velocity/velocyto/.config.vsh.yaml +++ b/target/docker/velocity/velocyto/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "velocyto" namespace: "velocity" - version: "1.0.1" + version: "1.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -228,6 +228,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/docker/velocity/velocyto" executable: "/home/runner/work/openpipeline/openpipeline/target/docker/velocity/velocyto/velocyto" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/docker/velocity/velocyto/velocyto b/target/docker/velocity/velocyto/velocyto index b34dbc494da..47bd5d258da 100755 --- a/target/docker/velocity/velocyto/velocyto +++ b/target/docker/velocity/velocyto/velocyto @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# velocyto 1.0.1 +# velocyto 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "velocyto 1.0.1" + echo "velocyto 1.0.2" echo "" echo "Runs the velocity analysis on a BAM file, outputting a loom file." echo "" @@ -445,10 +445,10 @@ RUN apt-get update && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component velocity velocyto" -LABEL org.opencontainers.image.created="2024-06-18T14:15:00Z" +LABEL org.opencontainers.image.created="2024-07-22T07:16:07Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="8ba584e550ac93c484a8b6ddea0c44618d02cf3f" -LABEL org.opencontainers.image.version="1.0.1" +LABEL org.opencontainers.image.revision="57add3ff137ac44d67bc7456cb9146bc6dc633cc" +LABEL org.opencontainers.image.version="1.0.2" VIASHDOCKER } @@ -603,7 +603,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "velocyto 1.0.1" + echo "velocyto 1.0.2" exit ;; --input) diff --git a/target/native/compression/compress_h5mu/.config.vsh.yaml b/target/native/compression/compress_h5mu/.config.vsh.yaml index 1acc0f50312..05b748459c0 100644 --- a/target/native/compression/compress_h5mu/.config.vsh.yaml +++ b/target/native/compression/compress_h5mu/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "compress_h5mu" namespace: "compression" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -171,6 +171,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/native/compression/compress_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/native/compression/compress_h5mu/compress_h5mu" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/native/compression/compress_h5mu/compress_h5mu b/target/native/compression/compress_h5mu/compress_h5mu index 929ba2761e6..0a108bb284b 100755 --- a/target/native/compression/compress_h5mu/compress_h5mu +++ b/target/native/compression/compress_h5mu/compress_h5mu @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# compress_h5mu 1.0.1 +# compress_h5mu 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "compress_h5mu 1.0.1" + echo "compress_h5mu 1.0.2" echo "" echo "Compress a MuData file." echo "" @@ -217,7 +217,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "compress_h5mu 1.0.1" + echo "compress_h5mu 1.0.2" exit ;; --input) diff --git a/target/native/compression/tar_extract/.config.vsh.yaml b/target/native/compression/tar_extract/.config.vsh.yaml index b46ecd5138c..d2176e9c874 100644 --- a/target/native/compression/tar_extract/.config.vsh.yaml +++ b/target/native/compression/tar_extract/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "tar_extract" namespace: "compression" - version: "1.0.1" + version: "1.0.2" arguments: - type: "file" name: "--input" @@ -107,6 +107,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/native/compression/tar_extract" executable: "/home/runner/work/openpipeline/openpipeline/target/native/compression/tar_extract/tar_extract" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/native/compression/tar_extract/tar_extract b/target/native/compression/tar_extract/tar_extract index ccd59e01b4a..322335c5a99 100755 --- a/target/native/compression/tar_extract/tar_extract +++ b/target/native/compression/tar_extract/tar_extract @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# tar_extract 1.0.1 +# tar_extract 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -170,7 +170,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "tar_extract 1.0.1" + echo "tar_extract 1.0.2" echo "" echo "Extract files from a tar archive" echo "" @@ -222,7 +222,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "tar_extract 1.0.1" + echo "tar_extract 1.0.2" exit ;; --input) diff --git a/target/native/dataflow/concat/.config.vsh.yaml b/target/native/dataflow/concat/.config.vsh.yaml index 21c2ea5e181..edba2c247ce 100644 --- a/target/native/dataflow/concat/.config.vsh.yaml +++ b/target/native/dataflow/concat/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "concat" namespace: "dataflow" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -238,6 +238,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/native/dataflow/concat" executable: "/home/runner/work/openpipeline/openpipeline/target/native/dataflow/concat/concat" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/native/dataflow/concat/concat b/target/native/dataflow/concat/concat index b4eaa11e87a..d19e6784032 100755 --- a/target/native/dataflow/concat/concat +++ b/target/native/dataflow/concat/concat @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# concat 1.0.1 +# concat 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "concat 1.0.1" + echo "concat 1.0.2" echo "" echo "Concatenates several uni-modal samples in .h5mu files into a single file." echo "" @@ -246,7 +246,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "concat 1.0.1" + echo "concat 1.0.2" exit ;; --input) @@ -796,7 +796,15 @@ def split_conflicts_modalities(n_processes: int, samples: dict[str, anndata.AnnD output_index = getattr(output, matrix_name).index conflicts, concatenated_matrix = concatenate_matrices(n_processes, matrices, output_index) if concatenated_matrix.empty: - concatenated_matrix.index = output_index + concatenated_matrix.index = output_index + + # Even though we did not touch the varm and obsm matrices that were already present, + # the joining of observations might have caused a dtype change in these matrices as well + # so these also need to be casted to a writable dtype... + for multidim_name, multidim_data in getattr(output, f"{matrix_name}m").items(): + new_data = cast_to_writeable_dtype(multidim_data) if isinstance(multidim_data, pd.DataFrame) else multidim_data + getattr(output, f"{matrix_name}m")[multidim_name] = new_data + # Write the conflicts to the output for conflict_name, conflict_data in conflicts.items(): getattr(output, f"{matrix_name}m")[conflict_name] = conflict_data diff --git a/target/native/dataflow/concatenate_h5mu/.config.vsh.yaml b/target/native/dataflow/concatenate_h5mu/.config.vsh.yaml index 18b7143ceeb..e0502411876 100644 --- a/target/native/dataflow/concatenate_h5mu/.config.vsh.yaml +++ b/target/native/dataflow/concatenate_h5mu/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "concatenate_h5mu" namespace: "dataflow" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -238,6 +238,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/native/dataflow/concatenate_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/native/dataflow/concatenate_h5mu/concatenate_h5mu" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/native/dataflow/concatenate_h5mu/concatenate_h5mu b/target/native/dataflow/concatenate_h5mu/concatenate_h5mu index 32483f34629..1433b8c8183 100755 --- a/target/native/dataflow/concatenate_h5mu/concatenate_h5mu +++ b/target/native/dataflow/concatenate_h5mu/concatenate_h5mu @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# concatenate_h5mu 1.0.1 +# concatenate_h5mu 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "concatenate_h5mu 1.0.1" + echo "concatenate_h5mu 1.0.2" echo "" echo "Concatenates several uni-modal samples in .h5mu files into a single file." echo "" @@ -246,7 +246,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "concatenate_h5mu 1.0.1" + echo "concatenate_h5mu 1.0.2" exit ;; --input) @@ -796,7 +796,15 @@ def split_conflicts_modalities(n_processes: int, samples: dict[str, anndata.AnnD output_index = getattr(output, matrix_name).index conflicts, concatenated_matrix = concatenate_matrices(n_processes, matrices, output_index) if concatenated_matrix.empty: - concatenated_matrix.index = output_index + concatenated_matrix.index = output_index + + # Even though we did not touch the varm and obsm matrices that were already present, + # the joining of observations might have caused a dtype change in these matrices as well + # so these also need to be casted to a writable dtype... + for multidim_name, multidim_data in getattr(output, f"{matrix_name}m").items(): + new_data = cast_to_writeable_dtype(multidim_data) if isinstance(multidim_data, pd.DataFrame) else multidim_data + getattr(output, f"{matrix_name}m")[multidim_name] = new_data + # Write the conflicts to the output for conflict_name, conflict_data in conflicts.items(): getattr(output, f"{matrix_name}m")[conflict_name] = conflict_data diff --git a/target/native/dataflow/merge/.config.vsh.yaml b/target/native/dataflow/merge/.config.vsh.yaml index 3c25ef16d86..e5efa41e3e0 100644 --- a/target/native/dataflow/merge/.config.vsh.yaml +++ b/target/native/dataflow/merge/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "merge" namespace: "dataflow" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -187,6 +187,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/native/dataflow/merge" executable: "/home/runner/work/openpipeline/openpipeline/target/native/dataflow/merge/merge" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/native/dataflow/merge/merge b/target/native/dataflow/merge/merge index 1f869479c96..ff7b32c6dca 100755 --- a/target/native/dataflow/merge/merge +++ b/target/native/dataflow/merge/merge @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# merge 1.0.1 +# merge 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "merge 1.0.1" + echo "merge 1.0.2" echo "" echo "Combine one or more single-modality .h5mu files together into one .h5mu file." echo "" @@ -218,7 +218,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "merge 1.0.1" + echo "merge 1.0.2" exit ;; --input) diff --git a/target/native/dataflow/split_modalities/.config.vsh.yaml b/target/native/dataflow/split_modalities/.config.vsh.yaml index 6cf3cb9d1c9..2f1e80c8490 100644 --- a/target/native/dataflow/split_modalities/.config.vsh.yaml +++ b/target/native/dataflow/split_modalities/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "split_modalities" namespace: "dataflow" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -213,6 +213,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/native/dataflow/split_modalities" executable: "/home/runner/work/openpipeline/openpipeline/target/native/dataflow/split_modalities/split_modalities" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/native/dataflow/split_modalities/split_modalities b/target/native/dataflow/split_modalities/split_modalities index 75ea86071d0..15cb6487b3a 100755 --- a/target/native/dataflow/split_modalities/split_modalities +++ b/target/native/dataflow/split_modalities/split_modalities @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# split_modalities 1.0.1 +# split_modalities 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "split_modalities 1.0.1" + echo "split_modalities 1.0.2" echo "" echo "Split the modalities from a single .h5mu multimodal sample into seperate .h5mu" echo "files." @@ -225,7 +225,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "split_modalities 1.0.1" + echo "split_modalities 1.0.2" exit ;; --input) diff --git a/target/native/download/sync_test_resources/.config.vsh.yaml b/target/native/download/sync_test_resources/.config.vsh.yaml index ba9c7939d61..0f69e6424f4 100644 --- a/target/native/download/sync_test_resources/.config.vsh.yaml +++ b/target/native/download/sync_test_resources/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "sync_test_resources" namespace: "download" - version: "1.0.1" + version: "1.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -173,6 +173,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/native/download/sync_test_resources" executable: "/home/runner/work/openpipeline/openpipeline/target/native/download/sync_test_resources/sync_test_resources" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/native/download/sync_test_resources/sync_test_resources b/target/native/download/sync_test_resources/sync_test_resources index 84f0ff7ed83..0e2507ad224 100755 --- a/target/native/download/sync_test_resources/sync_test_resources +++ b/target/native/download/sync_test_resources/sync_test_resources @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# sync_test_resources 1.0.1 +# sync_test_resources 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "sync_test_resources 1.0.1" + echo "sync_test_resources 1.0.2" echo "" echo "Synchronise the test resources from s3://openpipelines-data to resources_test" echo "" @@ -235,7 +235,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "sync_test_resources 1.0.1" + echo "sync_test_resources 1.0.2" exit ;; --input) diff --git a/target/native/feature_annotation/score_genes_cell_cycle_scanpy/.config.vsh.yaml b/target/native/feature_annotation/score_genes_cell_cycle_scanpy/.config.vsh.yaml index 445030959ff..c457105d26d 100644 --- a/target/native/feature_annotation/score_genes_cell_cycle_scanpy/.config.vsh.yaml +++ b/target/native/feature_annotation/score_genes_cell_cycle_scanpy/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "score_genes_cell_cycle_scanpy" namespace: "feature_annotation" - version: "1.0.1" + version: "1.0.2" authors: - name: "Robrecht Cannoodt" info: @@ -339,6 +339,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/native/feature_annotation/score_genes_cell_cycle_scanpy" executable: "/home/runner/work/openpipeline/openpipeline/target/native/feature_annotation/score_genes_cell_cycle_scanpy/score_genes_cell_cycle_scanpy" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/native/feature_annotation/score_genes_cell_cycle_scanpy/score_genes_cell_cycle_scanpy b/target/native/feature_annotation/score_genes_cell_cycle_scanpy/score_genes_cell_cycle_scanpy index 3bd38ccc77b..48d522c40e1 100755 --- a/target/native/feature_annotation/score_genes_cell_cycle_scanpy/score_genes_cell_cycle_scanpy +++ b/target/native/feature_annotation/score_genes_cell_cycle_scanpy/score_genes_cell_cycle_scanpy @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# score_genes_cell_cycle_scanpy 1.0.1 +# score_genes_cell_cycle_scanpy 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "score_genes_cell_cycle_scanpy 1.0.1" + echo "score_genes_cell_cycle_scanpy 1.0.2" echo "" echo "Calculates the score associated to S phase and G2M phase and annotates the cell" echo "cycle phase for each cell, as implemented by scanpy." @@ -321,7 +321,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "score_genes_cell_cycle_scanpy 1.0.1" + echo "score_genes_cell_cycle_scanpy 1.0.2" exit ;; --input) diff --git a/target/native/integrate/scarches/.config.vsh.yaml b/target/native/integrate/scarches/.config.vsh.yaml index 2d37a114aa2..633a3b04993 100644 --- a/target/native/integrate/scarches/.config.vsh.yaml +++ b/target/native/integrate/scarches/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "scarches" namespace: "integrate" - version: "1.0.1" + version: "1.0.2" authors: - name: "Vladimir Shitov" info: @@ -336,6 +336,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/native/integrate/scarches" executable: "/home/runner/work/openpipeline/openpipeline/target/native/integrate/scarches/scarches" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/native/integrate/scarches/scarches b/target/native/integrate/scarches/scarches index 08022400670..c7e43bcc9aa 100755 --- a/target/native/integrate/scarches/scarches +++ b/target/native/integrate/scarches/scarches @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# scarches 1.0.1 +# scarches 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "scarches 1.0.1" + echo "scarches 1.0.2" echo "" echo "Performs reference mapping with scArches" echo "" @@ -294,7 +294,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "scarches 1.0.1" + echo "scarches 1.0.2" exit ;; --input) diff --git a/target/native/integrate/totalvi/.config.vsh.yaml b/target/native/integrate/totalvi/.config.vsh.yaml index eedee4c6953..d2f3c7cae70 100644 --- a/target/native/integrate/totalvi/.config.vsh.yaml +++ b/target/native/integrate/totalvi/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "totalvi" namespace: "integrate" - version: "1.0.1" + version: "1.0.2" authors: - name: "Vladimir Shitov" info: @@ -353,6 +353,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/native/integrate/totalvi" executable: "/home/runner/work/openpipeline/openpipeline/target/native/integrate/totalvi/totalvi" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/native/integrate/totalvi/totalvi b/target/native/integrate/totalvi/totalvi index 34ea51c6217..047bf89cdbe 100755 --- a/target/native/integrate/totalvi/totalvi +++ b/target/native/integrate/totalvi/totalvi @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# totalvi 1.0.1 +# totalvi 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "totalvi 1.0.1" + echo "totalvi 1.0.2" echo "" echo "Performs mapping to the reference by totalvi model:" echo "https://docs.scvi-tools.org/en/stable/tutorials/notebooks/scarches_scvi_tools.html#Reference-mapping-with-TOTALVI" @@ -294,7 +294,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "totalvi 1.0.1" + echo "totalvi 1.0.2" exit ;; --input) diff --git a/target/native/labels_transfer/knn/.config.vsh.yaml b/target/native/labels_transfer/knn/.config.vsh.yaml index 6d1a1f0409c..4c6feaa39e7 100644 --- a/target/native/labels_transfer/knn/.config.vsh.yaml +++ b/target/native/labels_transfer/knn/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "knn" namespace: "labels_transfer" - version: "1.0.1" + version: "1.0.2" authors: - name: "Vladimir Shitov" roles: @@ -384,6 +384,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/native/labels_transfer/knn" executable: "/home/runner/work/openpipeline/openpipeline/target/native/labels_transfer/knn/knn" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/native/labels_transfer/knn/knn b/target/native/labels_transfer/knn/knn index de5d6d7831e..7528d41c739 100755 --- a/target/native/labels_transfer/knn/knn +++ b/target/native/labels_transfer/knn/knn @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# knn 1.0.1 +# knn 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "knn 1.0.1" + echo "knn 1.0.2" echo "" echo "Performs label transfer from reference to query using KNN classifier" echo "" @@ -270,7 +270,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "knn 1.0.1" + echo "knn 1.0.2" exit ;; --input) diff --git a/target/native/labels_transfer/xgboost/.config.vsh.yaml b/target/native/labels_transfer/xgboost/.config.vsh.yaml index 1e3e4eff3a6..3382b67fe39 100644 --- a/target/native/labels_transfer/xgboost/.config.vsh.yaml +++ b/target/native/labels_transfer/xgboost/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "xgboost" namespace: "labels_transfer" - version: "1.0.1" + version: "1.0.2" authors: - name: "Vladimir Shitov" roles: @@ -599,6 +599,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/native/labels_transfer/xgboost" executable: "/home/runner/work/openpipeline/openpipeline/target/native/labels_transfer/xgboost/xgboost" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/native/labels_transfer/xgboost/xgboost b/target/native/labels_transfer/xgboost/xgboost index 2ce77c4af04..325d5fc45d6 100755 --- a/target/native/labels_transfer/xgboost/xgboost +++ b/target/native/labels_transfer/xgboost/xgboost @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# xgboost 1.0.1 +# xgboost 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "xgboost 1.0.1" + echo "xgboost 1.0.2" echo "" echo "Performs label transfer from reference to query using XGBoost classifier" echo "" @@ -397,7 +397,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "xgboost 1.0.1" + echo "xgboost 1.0.2" exit ;; --input) diff --git a/target/native/metadata/add_id/.config.vsh.yaml b/target/native/metadata/add_id/.config.vsh.yaml index 362f48606b1..9f47e410a37 100644 --- a/target/native/metadata/add_id/.config.vsh.yaml +++ b/target/native/metadata/add_id/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "add_id" namespace: "metadata" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -209,6 +209,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/native/metadata/add_id" executable: "/home/runner/work/openpipeline/openpipeline/target/native/metadata/add_id/add_id" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/native/metadata/add_id/add_id b/target/native/metadata/add_id/add_id index 50133a1e0ae..e528ae7fe5b 100755 --- a/target/native/metadata/add_id/add_id +++ b/target/native/metadata/add_id/add_id @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# add_id 1.0.1 +# add_id 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "add_id 1.0.1" + echo "add_id 1.0.2" echo "" echo "Add id of .obs. Also allows to make .obs_names (the .obs index) unique" echo "by prefixing the values with an unique id per .h5mu file." @@ -231,7 +231,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "add_id 1.0.1" + echo "add_id 1.0.2" exit ;; --input) diff --git a/target/native/metadata/grep_annotation_column/.config.vsh.yaml b/target/native/metadata/grep_annotation_column/.config.vsh.yaml index ff14f032bc6..43761e1ae33 100644 --- a/target/native/metadata/grep_annotation_column/.config.vsh.yaml +++ b/target/native/metadata/grep_annotation_column/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "grep_annotation_column" namespace: "metadata" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -267,6 +267,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/native/metadata/grep_annotation_column" executable: "/home/runner/work/openpipeline/openpipeline/target/native/metadata/grep_annotation_column/grep_annotation_column" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/native/metadata/grep_annotation_column/grep_annotation_column b/target/native/metadata/grep_annotation_column/grep_annotation_column index 6b147b2ae47..381f0272bc2 100755 --- a/target/native/metadata/grep_annotation_column/grep_annotation_column +++ b/target/native/metadata/grep_annotation_column/grep_annotation_column @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# grep_annotation_column 1.0.1 +# grep_annotation_column 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "grep_annotation_column 1.0.1" + echo "grep_annotation_column 1.0.2" echo "" echo "Perform a regex lookup on a column from the annotation matrices .obs or .var." echo "The annotation matrix can originate from either a modality, or all modalities" @@ -264,7 +264,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "grep_annotation_column 1.0.1" + echo "grep_annotation_column 1.0.2" exit ;; --input) diff --git a/target/native/transform/scale/.config.vsh.yaml b/target/native/transform/scale/.config.vsh.yaml index baef53c1f93..5a28e2ebdf1 100644 --- a/target/native/transform/scale/.config.vsh.yaml +++ b/target/native/transform/scale/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "scale" namespace: "transform" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -210,6 +210,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/native/transform/scale" executable: "/home/runner/work/openpipeline/openpipeline/target/native/transform/scale/scale" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/native/transform/scale/scale b/target/native/transform/scale/scale index 9df871e635a..9351c6c4f2a 100755 --- a/target/native/transform/scale/scale +++ b/target/native/transform/scale/scale @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# scale 1.0.1 +# scale 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "scale 1.0.1" + echo "scale 1.0.2" echo "" echo "Scale data to unit variance and zero mean." echo "" @@ -233,7 +233,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "scale 1.0.1" + echo "scale 1.0.2" exit ;; --input) diff --git a/target/native/velocity/scvelo/.config.vsh.yaml b/target/native/velocity/scvelo/.config.vsh.yaml index c7077e8b5e6..f53bc7bc293 100644 --- a/target/native/velocity/scvelo/.config.vsh.yaml +++ b/target/native/velocity/scvelo/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "scvelo" namespace: "velocity" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -282,6 +282,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/native/velocity/scvelo" executable: "/home/runner/work/openpipeline/openpipeline/target/native/velocity/scvelo/scvelo" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/native/velocity/scvelo/scvelo b/target/native/velocity/scvelo/scvelo index 8324eb10ab2..e3c03e1f312 100755 --- a/target/native/velocity/scvelo/scvelo +++ b/target/native/velocity/scvelo/scvelo @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# scvelo 1.0.1 +# scvelo 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "scvelo 1.0.1" + echo "scvelo 1.0.2" echo "" echo "Inputs:" echo " --input" @@ -273,7 +273,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "scvelo 1.0.1" + echo "scvelo 1.0.2" exit ;; --input) diff --git a/target/native/velocity/velocyto/.config.vsh.yaml b/target/native/velocity/velocyto/.config.vsh.yaml index 5be9bd8c24f..1d184bdb9d6 100644 --- a/target/native/velocity/velocyto/.config.vsh.yaml +++ b/target/native/velocity/velocyto/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "velocyto" namespace: "velocity" - version: "1.0.1" + version: "1.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -228,6 +228,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/native/velocity/velocyto" executable: "/home/runner/work/openpipeline/openpipeline/target/native/velocity/velocyto/velocyto" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/native/velocity/velocyto/velocyto b/target/native/velocity/velocyto/velocyto index 305d1b6f31e..f07fd530545 100755 --- a/target/native/velocity/velocyto/velocyto +++ b/target/native/velocity/velocyto/velocyto @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# velocyto 1.0.1 +# velocyto 1.0.2 # # This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "velocyto 1.0.1" + echo "velocyto 1.0.2" echo "" echo "Runs the velocity analysis on a BAM file, outputting a loom file." echo "" @@ -232,7 +232,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "velocyto 1.0.1" + echo "velocyto 1.0.2" exit ;; --input) diff --git a/target/nextflow/annotate/popv/.config.vsh.yaml b/target/nextflow/annotate/popv/.config.vsh.yaml index 140ae609327..e0c243914fb 100644 --- a/target/nextflow/annotate/popv/.config.vsh.yaml +++ b/target/nextflow/annotate/popv/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "popv" namespace: "annotate" - version: "1.0.1" + version: "1.0.2" authors: - name: "Matthias Beyens" roles: @@ -352,6 +352,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/annotate/popv" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/annotate/popv/popv" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/annotate/popv/main.nf b/target/nextflow/annotate/popv/main.nf index a70d4b9a4bf..77eb08e2bfd 100644 --- a/target/nextflow/annotate/popv/main.nf +++ b/target/nextflow/annotate/popv/main.nf @@ -1,4 +1,4 @@ -// popv 1.0.1 +// popv 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2786,7 +2786,7 @@ meta = [ "functionality" : { "name" : "popv", "namespace" : "annotate", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Matthias Beyens", @@ -3233,9 +3233,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/annotate/popv", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/annotate/popv/nextflow.config b/target/nextflow/annotate/popv/nextflow.config index f8416c502b4..35309c17be0 100644 --- a/target/nextflow/annotate/popv/nextflow.config +++ b/target/nextflow/annotate/popv/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'annotate/popv' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Performs popular major vote cell typing on single cell sequence data using multiple algorithms. Note that this is a one-shot version of PopV.' author = 'Matthias Beyens, Robrecht Cannoodt' } diff --git a/target/nextflow/cluster/leiden/.config.vsh.yaml b/target/nextflow/cluster/leiden/.config.vsh.yaml index 583b297e84d..81ce14e794f 100644 --- a/target/nextflow/cluster/leiden/.config.vsh.yaml +++ b/target/nextflow/cluster/leiden/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "leiden" namespace: "cluster" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries De Maeyer" roles: @@ -230,6 +230,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/cluster/leiden" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/cluster/leiden/leiden" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/cluster/leiden/main.nf b/target/nextflow/cluster/leiden/main.nf index 714b9ce1578..052bedcd540 100644 --- a/target/nextflow/cluster/leiden/main.nf +++ b/target/nextflow/cluster/leiden/main.nf @@ -1,4 +1,4 @@ -// leiden 1.0.1 +// leiden 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "leiden", "namespace" : "cluster", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries De Maeyer", @@ -3067,9 +3067,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/cluster/leiden", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/cluster/leiden/nextflow.config b/target/nextflow/cluster/leiden/nextflow.config index fef4547e647..181422fd0b2 100644 --- a/target/nextflow/cluster/leiden/nextflow.config +++ b/target/nextflow/cluster/leiden/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'cluster/leiden' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Cluster cells using the [Leiden algorithm] [Traag18] implemented in the [Scanpy framework] [Wolf18]. \nLeiden is an improved version of the [Louvain algorithm] [Blondel08]. \nIt has been proposed for single-cell analysis by [Levine15] [Levine15]. \nThis requires having ran `neighbors/find_neighbors` or `neighbors/bbknn` first.\n\n[Blondel08]: Blondel et al. (2008), Fast unfolding of communities in large networks, J. Stat. Mech. \n[Levine15]: Levine et al. (2015), Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis, Cell. \n[Traag18]: Traag et al. (2018), From Louvain to Leiden: guaranteeing well-connected communities arXiv. \n[Wolf18]: Wolf et al. (2018), Scanpy: large-scale single-cell gene expression data analysis, Genome Biology. \n' author = 'Dries De Maeyer' } diff --git a/target/nextflow/compression/compress_h5mu/.config.vsh.yaml b/target/nextflow/compression/compress_h5mu/.config.vsh.yaml index 1faf448aec7..ecd6372080e 100644 --- a/target/nextflow/compression/compress_h5mu/.config.vsh.yaml +++ b/target/nextflow/compression/compress_h5mu/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "compress_h5mu" namespace: "compression" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -171,6 +171,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/compression/compress_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/compression/compress_h5mu/compress_h5mu" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/compression/compress_h5mu/main.nf b/target/nextflow/compression/compress_h5mu/main.nf index 595771ded32..7e2d4e731d8 100644 --- a/target/nextflow/compression/compress_h5mu/main.nf +++ b/target/nextflow/compression/compress_h5mu/main.nf @@ -1,4 +1,4 @@ -// compress_h5mu 1.0.1 +// compress_h5mu 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "compress_h5mu", "namespace" : "compression", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3013,9 +3013,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/compression/compress_h5mu", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/compression/compress_h5mu/nextflow.config b/target/nextflow/compression/compress_h5mu/nextflow.config index d31262e179a..911325f9d80 100644 --- a/target/nextflow/compression/compress_h5mu/nextflow.config +++ b/target/nextflow/compression/compress_h5mu/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'compression/compress_h5mu' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Compress a MuData file. \n' author = 'Dries Schaumont' } diff --git a/target/nextflow/convert/from_10xh5_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_10xh5_to_h5mu/.config.vsh.yaml index b66a1bd4cf7..e48969b004f 100644 --- a/target/nextflow/convert/from_10xh5_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/convert/from_10xh5_to_h5mu/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "from_10xh5_to_h5mu" namespace: "convert" - version: "1.0.1" + version: "1.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -277,6 +277,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_10xh5_to_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_10xh5_to_h5mu/from_10xh5_to_h5mu" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/convert/from_10xh5_to_h5mu/main.nf b/target/nextflow/convert/from_10xh5_to_h5mu/main.nf index 9baccc4510f..05d38754010 100644 --- a/target/nextflow/convert/from_10xh5_to_h5mu/main.nf +++ b/target/nextflow/convert/from_10xh5_to_h5mu/main.nf @@ -1,4 +1,4 @@ -// from_10xh5_to_h5mu 1.0.1 +// from_10xh5_to_h5mu 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "from_10xh5_to_h5mu", "namespace" : "convert", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -3167,9 +3167,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_10xh5_to_h5mu", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/convert/from_10xh5_to_h5mu/nextflow.config b/target/nextflow/convert/from_10xh5_to_h5mu/nextflow.config index 3b6f2c818b9..34f3966db92 100644 --- a/target/nextflow/convert/from_10xh5_to_h5mu/nextflow.config +++ b/target/nextflow/convert/from_10xh5_to_h5mu/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'convert/from_10xh5_to_h5mu' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Converts a 10x h5 into an h5mu file.\n' author = 'Robrecht Cannoodt' } diff --git a/target/nextflow/convert/from_10xmtx_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_10xmtx_to_h5mu/.config.vsh.yaml index 82ed1ccecd0..ab4bab0960a 100644 --- a/target/nextflow/convert/from_10xmtx_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/convert/from_10xmtx_to_h5mu/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "from_10xmtx_to_h5mu" namespace: "convert" - version: "1.0.1" + version: "1.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -171,6 +171,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_10xmtx_to_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_10xmtx_to_h5mu/from_10xmtx_to_h5mu" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/convert/from_10xmtx_to_h5mu/main.nf b/target/nextflow/convert/from_10xmtx_to_h5mu/main.nf index e6ec16e494f..68c1fc19d01 100644 --- a/target/nextflow/convert/from_10xmtx_to_h5mu/main.nf +++ b/target/nextflow/convert/from_10xmtx_to_h5mu/main.nf @@ -1,4 +1,4 @@ -// from_10xmtx_to_h5mu 1.0.1 +// from_10xmtx_to_h5mu 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "from_10xmtx_to_h5mu", "namespace" : "convert", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -3011,9 +3011,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_10xmtx_to_h5mu", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/convert/from_10xmtx_to_h5mu/nextflow.config b/target/nextflow/convert/from_10xmtx_to_h5mu/nextflow.config index a7559034c5a..8bf1765cedc 100644 --- a/target/nextflow/convert/from_10xmtx_to_h5mu/nextflow.config +++ b/target/nextflow/convert/from_10xmtx_to_h5mu/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'convert/from_10xmtx_to_h5mu' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Converts a 10x mtx into an h5mu file.\n' author = 'Robrecht Cannoodt' } diff --git a/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/.config.vsh.yaml b/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/.config.vsh.yaml index 82996f3b0c3..d95c24e561f 100644 --- a/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/.config.vsh.yaml +++ b/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "from_bd_to_10x_molecular_barcode_tags" namespace: "convert" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -162,6 +162,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/from_bd_to_10x_molecular_barcode_tags" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/main.nf b/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/main.nf index 8a9f193def4..a7e9e6cb650 100644 --- a/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/main.nf +++ b/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/main.nf @@ -1,4 +1,4 @@ -// from_bd_to_10x_molecular_barcode_tags 1.0.1 +// from_bd_to_10x_molecular_barcode_tags 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "from_bd_to_10x_molecular_barcode_tags", "namespace" : "convert", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -2993,9 +2993,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/nextflow.config b/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/nextflow.config index e7f36255abc..5d3e6a327cc 100644 --- a/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/nextflow.config +++ b/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'convert/from_bd_to_10x_molecular_barcode_tags' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Convert the molecular barcode sequence SAM tag from BD format (MA) to 10X format (UB).\n' author = 'Dries Schaumont' } diff --git a/target/nextflow/convert/from_bdrhap_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_bdrhap_to_h5mu/.config.vsh.yaml index 249a4f86043..62dc912906f 100644 --- a/target/nextflow/convert/from_bdrhap_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/convert/from_bdrhap_to_h5mu/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "from_bdrhap_to_h5mu" namespace: "convert" - version: "1.0.1" + version: "1.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -185,6 +185,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_bdrhap_to_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_bdrhap_to_h5mu/from_bdrhap_to_h5mu" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/convert/from_bdrhap_to_h5mu/main.nf b/target/nextflow/convert/from_bdrhap_to_h5mu/main.nf index 050beb5d4db..cf228ec8a7d 100644 --- a/target/nextflow/convert/from_bdrhap_to_h5mu/main.nf +++ b/target/nextflow/convert/from_bdrhap_to_h5mu/main.nf @@ -1,4 +1,4 @@ -// from_bdrhap_to_h5mu 1.0.1 +// from_bdrhap_to_h5mu 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "from_bdrhap_to_h5mu", "namespace" : "convert", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -3033,9 +3033,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_bdrhap_to_h5mu", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/convert/from_bdrhap_to_h5mu/nextflow.config b/target/nextflow/convert/from_bdrhap_to_h5mu/nextflow.config index 79119cc0b7e..798739f9a79 100644 --- a/target/nextflow/convert/from_bdrhap_to_h5mu/nextflow.config +++ b/target/nextflow/convert/from_bdrhap_to_h5mu/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'convert/from_bdrhap_to_h5mu' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Convert the output of a BD Rhapsody WTA pipeline to a MuData h5 file.\n' author = 'Robrecht Cannoodt' } diff --git a/target/nextflow/convert/from_cellranger_multi_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_cellranger_multi_to_h5mu/.config.vsh.yaml index 6dc66127bea..1f37deb6d7b 100644 --- a/target/nextflow/convert/from_cellranger_multi_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/convert/from_cellranger_multi_to_h5mu/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "from_cellranger_multi_to_h5mu" namespace: "convert" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -195,6 +195,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_cellranger_multi_to_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_cellranger_multi_to_h5mu/from_cellranger_multi_to_h5mu" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/convert/from_cellranger_multi_to_h5mu/main.nf b/target/nextflow/convert/from_cellranger_multi_to_h5mu/main.nf index 48c335eae7e..9746767d0d7 100644 --- a/target/nextflow/convert/from_cellranger_multi_to_h5mu/main.nf +++ b/target/nextflow/convert/from_cellranger_multi_to_h5mu/main.nf @@ -1,4 +1,4 @@ -// from_cellranger_multi_to_h5mu 1.0.1 +// from_cellranger_multi_to_h5mu 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "from_cellranger_multi_to_h5mu", "namespace" : "convert", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3036,9 +3036,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_cellranger_multi_to_h5mu", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/convert/from_cellranger_multi_to_h5mu/nextflow.config b/target/nextflow/convert/from_cellranger_multi_to_h5mu/nextflow.config index f6a24036f75..b8119e9bc3d 100644 --- a/target/nextflow/convert/from_cellranger_multi_to_h5mu/nextflow.config +++ b/target/nextflow/convert/from_cellranger_multi_to_h5mu/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'convert/from_cellranger_multi_to_h5mu' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Converts the output from cellranger multi to a single .h5mu file.\nBy default, will map the following library type names to modality names:\n - Gene Expression: rna\n - Peaks: atac\n - Antibody Capture: prot\n - VDJ: vdj\n - VDJ-T: vdj_t\n - VDJ-B: vdj_b\n - CRISPR Guide Capture: crispr\n - Multiplexing Capture: hashing\n\nOther library types have their whitepace removed and dashes replaced by\nunderscores to generate the modality name.\n\nCurrently does not allow parsing the output from cell barcode demultiplexing.\n' author = 'Dries Schaumont' } diff --git a/target/nextflow/convert/from_h5ad_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_h5ad_to_h5mu/.config.vsh.yaml index 8d933227ccb..607b4c066c7 100644 --- a/target/nextflow/convert/from_h5ad_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/convert/from_h5ad_to_h5mu/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "from_h5ad_to_h5mu" namespace: "convert" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries De Maeyer" roles: @@ -189,6 +189,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_h5ad_to_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_h5ad_to_h5mu/from_h5ad_to_h5mu" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/convert/from_h5ad_to_h5mu/main.nf b/target/nextflow/convert/from_h5ad_to_h5mu/main.nf index 7e29fc0cd72..debcee6ad1e 100644 --- a/target/nextflow/convert/from_h5ad_to_h5mu/main.nf +++ b/target/nextflow/convert/from_h5ad_to_h5mu/main.nf @@ -1,4 +1,4 @@ -// from_h5ad_to_h5mu 1.0.1 +// from_h5ad_to_h5mu 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "from_h5ad_to_h5mu", "namespace" : "convert", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries De Maeyer", @@ -3039,9 +3039,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_h5ad_to_h5mu", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/convert/from_h5ad_to_h5mu/nextflow.config b/target/nextflow/convert/from_h5ad_to_h5mu/nextflow.config index af80ccae770..9ea96d7bbdc 100644 --- a/target/nextflow/convert/from_h5ad_to_h5mu/nextflow.config +++ b/target/nextflow/convert/from_h5ad_to_h5mu/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'convert/from_h5ad_to_h5mu' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Converts a single layer h5ad file into a single MuData object\n' author = 'Dries De Maeyer' } diff --git a/target/nextflow/convert/from_h5mu_to_h5ad/.config.vsh.yaml b/target/nextflow/convert/from_h5mu_to_h5ad/.config.vsh.yaml index 7be40fadaec..70e00387d49 100644 --- a/target/nextflow/convert/from_h5mu_to_h5ad/.config.vsh.yaml +++ b/target/nextflow/convert/from_h5mu_to_h5ad/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "from_h5mu_to_h5ad" namespace: "convert" - version: "1.0.1" + version: "1.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -194,6 +194,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_h5mu_to_h5ad" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_h5mu_to_h5ad/from_h5mu_to_h5ad" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/convert/from_h5mu_to_h5ad/main.nf b/target/nextflow/convert/from_h5mu_to_h5ad/main.nf index e23b0d35a4d..4e5140f702f 100644 --- a/target/nextflow/convert/from_h5mu_to_h5ad/main.nf +++ b/target/nextflow/convert/from_h5mu_to_h5ad/main.nf @@ -1,4 +1,4 @@ -// from_h5mu_to_h5ad 1.0.1 +// from_h5mu_to_h5ad 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "from_h5mu_to_h5ad", "namespace" : "convert", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -3046,9 +3046,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_h5mu_to_h5ad", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/convert/from_h5mu_to_h5ad/nextflow.config b/target/nextflow/convert/from_h5mu_to_h5ad/nextflow.config index 714dcb17103..bfa6d9efe05 100644 --- a/target/nextflow/convert/from_h5mu_to_h5ad/nextflow.config +++ b/target/nextflow/convert/from_h5mu_to_h5ad/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'convert/from_h5mu_to_h5ad' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Converts a h5mu file into a h5ad file.\n' author = 'Robrecht Cannoodt' } diff --git a/target/nextflow/convert/from_h5mu_to_seurat/.config.vsh.yaml b/target/nextflow/convert/from_h5mu_to_seurat/.config.vsh.yaml index 37c0f45bcd4..9451a4dadcc 100644 --- a/target/nextflow/convert/from_h5mu_to_seurat/.config.vsh.yaml +++ b/target/nextflow/convert/from_h5mu_to_seurat/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "from_h5mu_to_seurat" namespace: "convert" - version: "1.0.1" + version: "1.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -186,6 +186,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_h5mu_to_seurat" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_h5mu_to_seurat/from_h5mu_to_seurat" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/convert/from_h5mu_to_seurat/main.nf b/target/nextflow/convert/from_h5mu_to_seurat/main.nf index 9d058976572..b0cf1bcfa35 100644 --- a/target/nextflow/convert/from_h5mu_to_seurat/main.nf +++ b/target/nextflow/convert/from_h5mu_to_seurat/main.nf @@ -1,4 +1,4 @@ -// from_h5mu_to_seurat 1.0.1 +// from_h5mu_to_seurat 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "from_h5mu_to_seurat", "namespace" : "convert", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -3029,9 +3029,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_h5mu_to_seurat", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/convert/from_h5mu_to_seurat/nextflow.config b/target/nextflow/convert/from_h5mu_to_seurat/nextflow.config index a96d2152fcf..0fe7d01edfe 100644 --- a/target/nextflow/convert/from_h5mu_to_seurat/nextflow.config +++ b/target/nextflow/convert/from_h5mu_to_seurat/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'convert/from_h5mu_to_seurat' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Converts an h5mu file into a Seurat file.\n\nRestrictions:\n - Only the intersection of cells is currently loaded into the Seurat object due to the object structure limitation.\n - Multimodal embeddings (global .obsm slot) are loaded with the assay.used field set to the default assay.\n - Embeddings names are changed in order to comply with R & Seurat requirements and conventions.\n - Feature names with underscores (\'_\') are automatically replaced with dashes (\'-\')\n - Seurat does not support global variables metadata /var.\n' author = 'Robrecht Cannoodt' } diff --git a/target/nextflow/convert/velocyto_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/velocyto_to_h5mu/.config.vsh.yaml index 0b720220e65..5a9302c32e1 100644 --- a/target/nextflow/convert/velocyto_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/convert/velocyto_to_h5mu/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "velocyto_to_h5mu" namespace: "convert" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -260,6 +260,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/velocyto_to_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/velocyto_to_h5mu/velocyto_to_h5mu" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/convert/velocyto_to_h5mu/main.nf b/target/nextflow/convert/velocyto_to_h5mu/main.nf index aa59370c2b3..f9a26a513a4 100644 --- a/target/nextflow/convert/velocyto_to_h5mu/main.nf +++ b/target/nextflow/convert/velocyto_to_h5mu/main.nf @@ -1,4 +1,4 @@ -// velocyto_to_h5mu 1.0.1 +// velocyto_to_h5mu 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2787,7 +2787,7 @@ meta = [ "functionality" : { "name" : "velocyto_to_h5mu", "namespace" : "convert", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3130,9 +3130,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/velocyto_to_h5mu", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/convert/velocyto_to_h5mu/nextflow.config b/target/nextflow/convert/velocyto_to_h5mu/nextflow.config index 4f05de97bac..ac1fc8c4ed9 100644 --- a/target/nextflow/convert/velocyto_to_h5mu/nextflow.config +++ b/target/nextflow/convert/velocyto_to_h5mu/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'convert/velocyto_to_h5mu' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Convert a velocyto loom file to a h5mu file.\n\nIf an input h5mu file is also provided, the velocity\nh5ad object will get added to that h5mu instead.\n' author = 'Dries Schaumont, Robrecht Cannoodt, Angela Oliveira Pisco' } diff --git a/target/nextflow/correction/cellbender_remove_background/.config.vsh.yaml b/target/nextflow/correction/cellbender_remove_background/.config.vsh.yaml index 6cf933ce5fe..eb9ac6825ce 100644 --- a/target/nextflow/correction/cellbender_remove_background/.config.vsh.yaml +++ b/target/nextflow/correction/cellbender_remove_background/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "cellbender_remove_background" namespace: "correction" - version: "1.0.1" + version: "1.0.2" argument_groups: - name: "Inputs" arguments: @@ -634,6 +634,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/correction/cellbender_remove_background" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/correction/cellbender_remove_background/cellbender_remove_background" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/correction/cellbender_remove_background/main.nf b/target/nextflow/correction/cellbender_remove_background/main.nf index aff7b535e99..d4dbc70b461 100644 --- a/target/nextflow/correction/cellbender_remove_background/main.nf +++ b/target/nextflow/correction/cellbender_remove_background/main.nf @@ -1,4 +1,4 @@ -// cellbender_remove_background 1.0.1 +// cellbender_remove_background 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2782,7 +2782,7 @@ meta = [ "functionality" : { "name" : "cellbender_remove_background", "namespace" : "correction", - "version" : "1.0.1", + "version" : "1.0.2", "argument_groups" : [ { "name" : "Inputs", @@ -3467,9 +3467,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/correction/cellbender_remove_background", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/correction/cellbender_remove_background/nextflow.config b/target/nextflow/correction/cellbender_remove_background/nextflow.config index 7d0debc5293..7f5feba19fe 100644 --- a/target/nextflow/correction/cellbender_remove_background/nextflow.config +++ b/target/nextflow/correction/cellbender_remove_background/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'correction/cellbender_remove_background' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Eliminating technical artifacts from high-throughput single-cell RNA sequencing data.\n\nThis module removes counts due to ambient RNA molecules and random barcode swapping from (raw) UMI-based scRNA-seq count matrices. \nAt the moment, only the count matrices produced by the CellRanger count pipeline is supported. Support for additional tools and protocols \nwill be added in the future. A quick start tutorial can be found here.\n\nFleming et al. 2022, bioRxiv.\n' } diff --git a/target/nextflow/correction/cellbender_remove_background_v0_2/.config.vsh.yaml b/target/nextflow/correction/cellbender_remove_background_v0_2/.config.vsh.yaml index 511199ec0ce..834a9a2cdb9 100644 --- a/target/nextflow/correction/cellbender_remove_background_v0_2/.config.vsh.yaml +++ b/target/nextflow/correction/cellbender_remove_background_v0_2/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "cellbender_remove_background_v0_2" namespace: "correction" - version: "1.0.1" + version: "1.0.2" argument_groups: - name: "Inputs" arguments: @@ -410,6 +410,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/correction/cellbender_remove_background_v0_2" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/correction/cellbender_remove_background_v0_2/cellbender_remove_background_v0_2" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/correction/cellbender_remove_background_v0_2/main.nf b/target/nextflow/correction/cellbender_remove_background_v0_2/main.nf index c3e23bbaf05..fae655094e5 100644 --- a/target/nextflow/correction/cellbender_remove_background_v0_2/main.nf +++ b/target/nextflow/correction/cellbender_remove_background_v0_2/main.nf @@ -1,4 +1,4 @@ -// cellbender_remove_background_v0_2 1.0.1 +// cellbender_remove_background_v0_2 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2782,7 +2782,7 @@ meta = [ "functionality" : { "name" : "cellbender_remove_background_v0_2", "namespace" : "correction", - "version" : "1.0.1", + "version" : "1.0.2", "argument_groups" : [ { "name" : "Inputs", @@ -3264,9 +3264,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/correction/cellbender_remove_background_v0_2", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/correction/cellbender_remove_background_v0_2/nextflow.config b/target/nextflow/correction/cellbender_remove_background_v0_2/nextflow.config index d02cc9cbb65..005b4d079c5 100644 --- a/target/nextflow/correction/cellbender_remove_background_v0_2/nextflow.config +++ b/target/nextflow/correction/cellbender_remove_background_v0_2/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'correction/cellbender_remove_background_v0_2' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Eliminating technical artifacts from high-throughput single-cell RNA sequencing data.\n\nThis module removes counts due to ambient RNA molecules and random barcode swapping from (raw) UMI-based scRNA-seq count matrices. \nAt the moment, only the count matrices produced by the CellRanger count pipeline is supported. Support for additional tools and protocols \nwill be added in the future. A quick start tutorial can be found here.\n\nFleming et al. 2022, bioRxiv.\n' } diff --git a/target/nextflow/dataflow/concat/.config.vsh.yaml b/target/nextflow/dataflow/concat/.config.vsh.yaml index 2109e19bd17..f0399b94cd9 100644 --- a/target/nextflow/dataflow/concat/.config.vsh.yaml +++ b/target/nextflow/dataflow/concat/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "concat" namespace: "dataflow" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -238,6 +238,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/dataflow/concat" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/dataflow/concat/concat" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/dataflow/concat/main.nf b/target/nextflow/dataflow/concat/main.nf index 4188c830f5e..820f1aab057 100644 --- a/target/nextflow/dataflow/concat/main.nf +++ b/target/nextflow/dataflow/concat/main.nf @@ -1,4 +1,4 @@ -// concat 1.0.1 +// concat 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "concat", "namespace" : "dataflow", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3090,9 +3090,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/dataflow/concat", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] @@ -3343,7 +3343,15 @@ def split_conflicts_modalities(n_processes: int, samples: dict[str, anndata.AnnD output_index = getattr(output, matrix_name).index conflicts, concatenated_matrix = concatenate_matrices(n_processes, matrices, output_index) if concatenated_matrix.empty: - concatenated_matrix.index = output_index + concatenated_matrix.index = output_index + + # Even though we did not touch the varm and obsm matrices that were already present, + # the joining of observations might have caused a dtype change in these matrices as well + # so these also need to be casted to a writable dtype... + for multidim_name, multidim_data in getattr(output, f"{matrix_name}m").items(): + new_data = cast_to_writeable_dtype(multidim_data) if isinstance(multidim_data, pd.DataFrame) else multidim_data + getattr(output, f"{matrix_name}m")[multidim_name] = new_data + # Write the conflicts to the output for conflict_name, conflict_data in conflicts.items(): getattr(output, f"{matrix_name}m")[conflict_name] = conflict_data diff --git a/target/nextflow/dataflow/concat/nextflow.config b/target/nextflow/dataflow/concat/nextflow.config index b0bbd02395c..082b0f07f23 100644 --- a/target/nextflow/dataflow/concat/nextflow.config +++ b/target/nextflow/dataflow/concat/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'dataflow/concat' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Concatenates several uni-modal samples in .h5mu files into a single file.\n' author = 'Dries Schaumont' } diff --git a/target/nextflow/dataflow/concatenate_h5mu/.config.vsh.yaml b/target/nextflow/dataflow/concatenate_h5mu/.config.vsh.yaml index 8f29adf2a5e..5593be52f93 100644 --- a/target/nextflow/dataflow/concatenate_h5mu/.config.vsh.yaml +++ b/target/nextflow/dataflow/concatenate_h5mu/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "concatenate_h5mu" namespace: "dataflow" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -238,6 +238,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/dataflow/concatenate_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/dataflow/concatenate_h5mu/concatenate_h5mu" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/dataflow/concatenate_h5mu/main.nf b/target/nextflow/dataflow/concatenate_h5mu/main.nf index 28fa792cdaf..b26320cfa70 100644 --- a/target/nextflow/dataflow/concatenate_h5mu/main.nf +++ b/target/nextflow/dataflow/concatenate_h5mu/main.nf @@ -1,4 +1,4 @@ -// concatenate_h5mu 1.0.1 +// concatenate_h5mu 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "concatenate_h5mu", "namespace" : "dataflow", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3090,9 +3090,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/dataflow/concatenate_h5mu", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] @@ -3343,7 +3343,15 @@ def split_conflicts_modalities(n_processes: int, samples: dict[str, anndata.AnnD output_index = getattr(output, matrix_name).index conflicts, concatenated_matrix = concatenate_matrices(n_processes, matrices, output_index) if concatenated_matrix.empty: - concatenated_matrix.index = output_index + concatenated_matrix.index = output_index + + # Even though we did not touch the varm and obsm matrices that were already present, + # the joining of observations might have caused a dtype change in these matrices as well + # so these also need to be casted to a writable dtype... + for multidim_name, multidim_data in getattr(output, f"{matrix_name}m").items(): + new_data = cast_to_writeable_dtype(multidim_data) if isinstance(multidim_data, pd.DataFrame) else multidim_data + getattr(output, f"{matrix_name}m")[multidim_name] = new_data + # Write the conflicts to the output for conflict_name, conflict_data in conflicts.items(): getattr(output, f"{matrix_name}m")[conflict_name] = conflict_data diff --git a/target/nextflow/dataflow/concatenate_h5mu/nextflow.config b/target/nextflow/dataflow/concatenate_h5mu/nextflow.config index c8b5888c10c..1ee812274c3 100644 --- a/target/nextflow/dataflow/concatenate_h5mu/nextflow.config +++ b/target/nextflow/dataflow/concatenate_h5mu/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'dataflow/concatenate_h5mu' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Concatenates several uni-modal samples in .h5mu files into a single file.\n' author = 'Dries Schaumont' } diff --git a/target/nextflow/dataflow/merge/.config.vsh.yaml b/target/nextflow/dataflow/merge/.config.vsh.yaml index cad927df8da..49d68e69077 100644 --- a/target/nextflow/dataflow/merge/.config.vsh.yaml +++ b/target/nextflow/dataflow/merge/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "merge" namespace: "dataflow" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -187,6 +187,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/dataflow/merge" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/dataflow/merge/merge" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/dataflow/merge/main.nf b/target/nextflow/dataflow/merge/main.nf index a8ce866b8a2..406b6ea5f7f 100644 --- a/target/nextflow/dataflow/merge/main.nf +++ b/target/nextflow/dataflow/merge/main.nf @@ -1,4 +1,4 @@ -// merge 1.0.1 +// merge 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "merge", "namespace" : "dataflow", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3039,9 +3039,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/dataflow/merge", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/dataflow/merge/nextflow.config b/target/nextflow/dataflow/merge/nextflow.config index deb2ad0d302..4fe4f80d653 100644 --- a/target/nextflow/dataflow/merge/nextflow.config +++ b/target/nextflow/dataflow/merge/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'dataflow/merge' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Combine one or more single-modality .h5mu files together into one .h5mu file.\n' author = 'Dries Schaumont' } diff --git a/target/nextflow/dataflow/split_modalities/.config.vsh.yaml b/target/nextflow/dataflow/split_modalities/.config.vsh.yaml index 4209730f2b5..35db5584a8f 100644 --- a/target/nextflow/dataflow/split_modalities/.config.vsh.yaml +++ b/target/nextflow/dataflow/split_modalities/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "split_modalities" namespace: "dataflow" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -213,6 +213,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/dataflow/split_modalities" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/dataflow/split_modalities/split_modalities" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/dataflow/split_modalities/main.nf b/target/nextflow/dataflow/split_modalities/main.nf index 9565f2f8485..73f3f60807d 100644 --- a/target/nextflow/dataflow/split_modalities/main.nf +++ b/target/nextflow/dataflow/split_modalities/main.nf @@ -1,4 +1,4 @@ -// split_modalities 1.0.1 +// split_modalities 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2786,7 +2786,7 @@ meta = [ "functionality" : { "name" : "split_modalities", "namespace" : "dataflow", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3071,9 +3071,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/dataflow/split_modalities", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/dataflow/split_modalities/nextflow.config b/target/nextflow/dataflow/split_modalities/nextflow.config index 1a32a1d60b3..a7f13616f39 100644 --- a/target/nextflow/dataflow/split_modalities/nextflow.config +++ b/target/nextflow/dataflow/split_modalities/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'dataflow/split_modalities' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Split the modalities from a single .h5mu multimodal sample into seperate .h5mu files. \n' author = 'Dries Schaumont, Robrecht Cannoodt' } diff --git a/target/nextflow/demux/bcl2fastq/.config.vsh.yaml b/target/nextflow/demux/bcl2fastq/.config.vsh.yaml index ee16b1531ce..2b963d6c961 100644 --- a/target/nextflow/demux/bcl2fastq/.config.vsh.yaml +++ b/target/nextflow/demux/bcl2fastq/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "bcl2fastq" namespace: "demux" - version: "1.0.1" + version: "1.0.2" authors: - name: "Toni Verbeiren" roles: @@ -177,6 +177,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/demux/bcl2fastq" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/demux/bcl2fastq/bcl2fastq" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/demux/bcl2fastq/main.nf b/target/nextflow/demux/bcl2fastq/main.nf index c930949b9f1..1314ee21ead 100644 --- a/target/nextflow/demux/bcl2fastq/main.nf +++ b/target/nextflow/demux/bcl2fastq/main.nf @@ -1,4 +1,4 @@ -// bcl2fastq 1.0.1 +// bcl2fastq 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "bcl2fastq", "namespace" : "demux", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Toni Verbeiren", @@ -3012,9 +3012,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/demux/bcl2fastq", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/demux/bcl2fastq/nextflow.config b/target/nextflow/demux/bcl2fastq/nextflow.config index d0dc4c3146a..5578c7ae009 100644 --- a/target/nextflow/demux/bcl2fastq/nextflow.config +++ b/target/nextflow/demux/bcl2fastq/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'demux/bcl2fastq' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Convert bcl files to fastq files using bcl2fastq.\n' author = 'Toni Verbeiren' } diff --git a/target/nextflow/demux/bcl_convert/.config.vsh.yaml b/target/nextflow/demux/bcl_convert/.config.vsh.yaml index 3810f04bdb5..0a22e2d7501 100644 --- a/target/nextflow/demux/bcl_convert/.config.vsh.yaml +++ b/target/nextflow/demux/bcl_convert/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "bcl_convert" namespace: "demux" - version: "1.0.1" + version: "1.0.2" authors: - name: "Toni Verbeiren" roles: @@ -197,6 +197,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/demux/bcl_convert" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/demux/bcl_convert/bcl_convert" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/demux/bcl_convert/main.nf b/target/nextflow/demux/bcl_convert/main.nf index 6746002ce3c..d78f13178f9 100644 --- a/target/nextflow/demux/bcl_convert/main.nf +++ b/target/nextflow/demux/bcl_convert/main.nf @@ -1,4 +1,4 @@ -// bcl_convert 1.0.1 +// bcl_convert 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2786,7 +2786,7 @@ meta = [ "functionality" : { "name" : "bcl_convert", "namespace" : "demux", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Toni Verbeiren", @@ -3040,9 +3040,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/demux/bcl_convert", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/demux/bcl_convert/nextflow.config b/target/nextflow/demux/bcl_convert/nextflow.config index aa81c2e1c4b..82bb33fc843 100644 --- a/target/nextflow/demux/bcl_convert/nextflow.config +++ b/target/nextflow/demux/bcl_convert/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'demux/bcl_convert' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Convert bcl files to fastq files using bcl-convert.\nInformation about upgrading from bcl2fastq via\nhttps://emea.support.illumina.com/bulletins/2020/10/upgrading-from-bcl2fastq-to-bcl-convert.html\nand https://support.illumina.com/sequencing/sequencing_software/bcl-convert/compatibility.html\n' author = 'Toni Verbeiren, Marijke Van Moerbeke' } diff --git a/target/nextflow/demux/cellranger_mkfastq/.config.vsh.yaml b/target/nextflow/demux/cellranger_mkfastq/.config.vsh.yaml index e1fb70b835d..0820f08aff4 100644 --- a/target/nextflow/demux/cellranger_mkfastq/.config.vsh.yaml +++ b/target/nextflow/demux/cellranger_mkfastq/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "cellranger_mkfastq" namespace: "demux" - version: "1.0.1" + version: "1.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -211,6 +211,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/demux/cellranger_mkfastq" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/demux/cellranger_mkfastq/cellranger_mkfastq" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/demux/cellranger_mkfastq/main.nf b/target/nextflow/demux/cellranger_mkfastq/main.nf index 94e9899e0f7..a54e5d8ee21 100644 --- a/target/nextflow/demux/cellranger_mkfastq/main.nf +++ b/target/nextflow/demux/cellranger_mkfastq/main.nf @@ -1,4 +1,4 @@ -// cellranger_mkfastq 1.0.1 +// cellranger_mkfastq 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2787,7 +2787,7 @@ meta = [ "functionality" : { "name" : "cellranger_mkfastq", "namespace" : "demux", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Angela Oliveira Pisco", @@ -3069,9 +3069,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/demux/cellranger_mkfastq", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/demux/cellranger_mkfastq/nextflow.config b/target/nextflow/demux/cellranger_mkfastq/nextflow.config index 1b1698a23c9..43ddf4dd0d6 100644 --- a/target/nextflow/demux/cellranger_mkfastq/nextflow.config +++ b/target/nextflow/demux/cellranger_mkfastq/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'demux/cellranger_mkfastq' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Demultiplex raw sequencing data' author = 'Angela Oliveira Pisco, Samuel D\'Souza, Robrecht Cannoodt' } diff --git a/target/nextflow/dimred/pca/.config.vsh.yaml b/target/nextflow/dimred/pca/.config.vsh.yaml index 872f8c23ac3..509c2f51dc2 100644 --- a/target/nextflow/dimred/pca/.config.vsh.yaml +++ b/target/nextflow/dimred/pca/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "pca" namespace: "dimred" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries De Maeyer" roles: @@ -258,6 +258,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/dimred/pca" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/dimred/pca/pca" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/dimred/pca/main.nf b/target/nextflow/dimred/pca/main.nf index a572a8ade17..eae5693c417 100644 --- a/target/nextflow/dimred/pca/main.nf +++ b/target/nextflow/dimred/pca/main.nf @@ -1,4 +1,4 @@ -// pca 1.0.1 +// pca 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "pca", "namespace" : "dimred", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries De Maeyer", @@ -3110,9 +3110,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/dimred/pca", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/dimred/pca/nextflow.config b/target/nextflow/dimred/pca/nextflow.config index a3ccb98dd58..25fca89f73f 100644 --- a/target/nextflow/dimred/pca/nextflow.config +++ b/target/nextflow/dimred/pca/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'dimred/pca' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Computes PCA coordinates, loadings and variance decomposition. Uses the implementation of scikit-learn [Pedregosa11].\n' author = 'Dries De Maeyer' } diff --git a/target/nextflow/dimred/tsne/.config.vsh.yaml b/target/nextflow/dimred/tsne/.config.vsh.yaml index 1e5eb8c9bc2..9cd46fe45ed 100644 --- a/target/nextflow/dimred/tsne/.config.vsh.yaml +++ b/target/nextflow/dimred/tsne/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "tsne" namespace: "dimred" - version: "1.0.1" + version: "1.0.2" authors: - name: "Jakub Majercik" roles: @@ -311,6 +311,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/dimred/tsne" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/dimred/tsne/tsne" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/dimred/tsne/main.nf b/target/nextflow/dimred/tsne/main.nf index debb6505d00..1e8ae083eba 100644 --- a/target/nextflow/dimred/tsne/main.nf +++ b/target/nextflow/dimred/tsne/main.nf @@ -1,4 +1,4 @@ -// tsne 1.0.1 +// tsne 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "tsne", "namespace" : "dimred", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Jakub Majercik", @@ -3171,9 +3171,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/dimred/tsne", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/dimred/tsne/nextflow.config b/target/nextflow/dimred/tsne/nextflow.config index e57dbdbfb58..8f19b2b62d0 100644 --- a/target/nextflow/dimred/tsne/nextflow.config +++ b/target/nextflow/dimred/tsne/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'dimred/tsne' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 't-SNE (t-Distributed Stochastic Neighbor Embedding) is a dimensionality reduction technique used to visualize high-dimensional data in a low-dimensional space, revealing patterns and clusters by preserving local data similarities.\n' author = 'Jakub Majercik' } diff --git a/target/nextflow/dimred/umap/.config.vsh.yaml b/target/nextflow/dimred/umap/.config.vsh.yaml index 7c67771bcba..3ee4f1415bc 100644 --- a/target/nextflow/dimred/umap/.config.vsh.yaml +++ b/target/nextflow/dimred/umap/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "umap" namespace: "dimred" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries De Maeyer" roles: @@ -317,6 +317,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/dimred/umap" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/dimred/umap/umap" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/dimred/umap/main.nf b/target/nextflow/dimred/umap/main.nf index b2205715dee..fc3d6e7c034 100644 --- a/target/nextflow/dimred/umap/main.nf +++ b/target/nextflow/dimred/umap/main.nf @@ -1,4 +1,4 @@ -// umap 1.0.1 +// umap 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "umap", "namespace" : "dimred", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries De Maeyer", @@ -3167,9 +3167,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/dimred/umap", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/dimred/umap/nextflow.config b/target/nextflow/dimred/umap/nextflow.config index 2507c3c9f16..000aab89ab5 100644 --- a/target/nextflow/dimred/umap/nextflow.config +++ b/target/nextflow/dimred/umap/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'dimred/umap' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'UMAP (Uniform Manifold Approximation and Projection) is a manifold learning technique suitable for visualizing high-dimensional data. Besides tending to be faster than tSNE, it optimizes the embedding such that it best reflects the topology of the data, which we represent throughout Scanpy using a neighborhood graph. tSNE, by contrast, optimizes the distribution of nearest-neighbor distances in the embedding such that these best match the distribution of distances in the high-dimensional space. We use the implementation of umap-learn [McInnes18]. For a few comparisons of UMAP with tSNE, see this preprint.\n' author = 'Dries De Maeyer' } diff --git a/target/nextflow/download/download_file/.config.vsh.yaml b/target/nextflow/download/download_file/.config.vsh.yaml index 39e5b706793..705eff2c817 100644 --- a/target/nextflow/download/download_file/.config.vsh.yaml +++ b/target/nextflow/download/download_file/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "download_file" namespace: "download" - version: "1.0.1" + version: "1.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -141,6 +141,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/download/download_file" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/download/download_file/download_file" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/download/download_file/main.nf b/target/nextflow/download/download_file/main.nf index ad6ea1cb56b..9ebf0346473 100644 --- a/target/nextflow/download/download_file/main.nf +++ b/target/nextflow/download/download_file/main.nf @@ -1,4 +1,4 @@ -// download_file 1.0.1 +// download_file 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "download_file", "namespace" : "download", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -2963,9 +2963,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/download/download_file", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/download/download_file/nextflow.config b/target/nextflow/download/download_file/nextflow.config index d3f671a244e..2cc7e145e57 100644 --- a/target/nextflow/download/download_file/nextflow.config +++ b/target/nextflow/download/download_file/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'download/download_file' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Download a file.\n' author = 'Robrecht Cannoodt' } diff --git a/target/nextflow/download/sync_test_resources/.config.vsh.yaml b/target/nextflow/download/sync_test_resources/.config.vsh.yaml index 5a321cca7f3..64c8892f52b 100644 --- a/target/nextflow/download/sync_test_resources/.config.vsh.yaml +++ b/target/nextflow/download/sync_test_resources/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "sync_test_resources" namespace: "download" - version: "1.0.1" + version: "1.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -173,6 +173,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/download/sync_test_resources" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/download/sync_test_resources/sync_test_resources" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/download/sync_test_resources/main.nf b/target/nextflow/download/sync_test_resources/main.nf index b04ab4e3f9d..46b208b7b7d 100644 --- a/target/nextflow/download/sync_test_resources/main.nf +++ b/target/nextflow/download/sync_test_resources/main.nf @@ -1,4 +1,4 @@ -// sync_test_resources 1.0.1 +// sync_test_resources 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "sync_test_resources", "namespace" : "download", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -3002,9 +3002,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/download/sync_test_resources", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/download/sync_test_resources/nextflow.config b/target/nextflow/download/sync_test_resources/nextflow.config index 7cc7f09e161..83f3cfd1a2b 100644 --- a/target/nextflow/download/sync_test_resources/nextflow.config +++ b/target/nextflow/download/sync_test_resources/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'download/sync_test_resources' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Synchronise the test resources from s3://openpipelines-data to resources_test' author = 'Robrecht Cannoodt' } diff --git a/target/nextflow/feature_annotation/highly_variable_features_scanpy/.config.vsh.yaml b/target/nextflow/feature_annotation/highly_variable_features_scanpy/.config.vsh.yaml index 146d6e4eff3..9811ec0514b 100644 --- a/target/nextflow/feature_annotation/highly_variable_features_scanpy/.config.vsh.yaml +++ b/target/nextflow/feature_annotation/highly_variable_features_scanpy/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "highly_variable_features_scanpy" namespace: "feature_annotation" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries De Maeyer" roles: @@ -352,6 +352,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/feature_annotation/highly_variable_features_scanpy" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/feature_annotation/highly_variable_features_scanpy/highly_variable_features_scanpy" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/feature_annotation/highly_variable_features_scanpy/main.nf b/target/nextflow/feature_annotation/highly_variable_features_scanpy/main.nf index 92d8dba5d5a..f5c71ff461f 100644 --- a/target/nextflow/feature_annotation/highly_variable_features_scanpy/main.nf +++ b/target/nextflow/feature_annotation/highly_variable_features_scanpy/main.nf @@ -1,4 +1,4 @@ -// highly_variable_features_scanpy 1.0.1 +// highly_variable_features_scanpy 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2786,7 +2786,7 @@ meta = [ "functionality" : { "name" : "highly_variable_features_scanpy", "namespace" : "feature_annotation", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries De Maeyer", @@ -3194,9 +3194,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/feature_annotation/highly_variable_features_scanpy", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/feature_annotation/highly_variable_features_scanpy/nextflow.config b/target/nextflow/feature_annotation/highly_variable_features_scanpy/nextflow.config index a36642b950f..088bb3d593d 100644 --- a/target/nextflow/feature_annotation/highly_variable_features_scanpy/nextflow.config +++ b/target/nextflow/feature_annotation/highly_variable_features_scanpy/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'feature_annotation/highly_variable_features_scanpy' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Annotate highly variable features [Satija15] [Zheng17] [Stuart19].\n\nExpects logarithmized data, except when flavor=\'seurat_v3\' in which count data is expected.\n\nDepending on flavor, this reproduces the R-implementations of Seurat [Satija15], Cell Ranger [Zheng17], and Seurat v3 [Stuart19].\n\nFor the dispersion-based methods ([Satija15] and [Zheng17]), the normalized dispersion is obtained by scaling with the mean and standard deviation of the dispersions for features falling into a given bin for mean expression of features. This means that for each bin of mean expression, highly variable features are selected.\n\nFor [Stuart19], a normalized variance for each feature is computed. First, the data are standardized (i.e., z-score normalization per feature) with a regularized standard deviation. Next, the normalized variance is computed as the variance of each feature after the transformation. Features are ranked by the normalized variance.\n' author = 'Dries De Maeyer, Robrecht Cannoodt' } diff --git a/target/nextflow/files/make_params/.config.vsh.yaml b/target/nextflow/files/make_params/.config.vsh.yaml index ce679c8c9ea..0b496d1d974 100644 --- a/target/nextflow/files/make_params/.config.vsh.yaml +++ b/target/nextflow/files/make_params/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "make_params" namespace: "files" - version: "1.0.1" + version: "1.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -223,6 +223,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/files/make_params" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/files/make_params/make_params" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/files/make_params/main.nf b/target/nextflow/files/make_params/main.nf index 09113c4dc05..3a7f5b0423c 100644 --- a/target/nextflow/files/make_params/main.nf +++ b/target/nextflow/files/make_params/main.nf @@ -1,4 +1,4 @@ -// make_params 1.0.1 +// make_params 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2786,7 +2786,7 @@ meta = [ "functionality" : { "name" : "make_params", "namespace" : "files", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Angela Oliveira Pisco", @@ -3069,9 +3069,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/files/make_params", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/files/make_params/nextflow.config b/target/nextflow/files/make_params/nextflow.config index a705e01fd14..f06e1f24a78 100644 --- a/target/nextflow/files/make_params/nextflow.config +++ b/target/nextflow/files/make_params/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'files/make_params' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Looks for files in a directory and turn it in a params file.' author = 'Angela Oliveira Pisco, Robrecht Cannoodt' } diff --git a/target/nextflow/filter/delimit_fraction/.config.vsh.yaml b/target/nextflow/filter/delimit_fraction/.config.vsh.yaml index a57211a3ddd..2609ddd6ee5 100644 --- a/target/nextflow/filter/delimit_fraction/.config.vsh.yaml +++ b/target/nextflow/filter/delimit_fraction/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "delimit_fraction" namespace: "filter" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -253,6 +253,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/delimit_fraction" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/delimit_fraction/delimit_fraction" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/filter/delimit_fraction/main.nf b/target/nextflow/filter/delimit_fraction/main.nf index c9a939d8697..0a03b861ff0 100644 --- a/target/nextflow/filter/delimit_fraction/main.nf +++ b/target/nextflow/filter/delimit_fraction/main.nf @@ -1,4 +1,4 @@ -// delimit_fraction 1.0.1 +// delimit_fraction 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "delimit_fraction", "namespace" : "filter", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3116,9 +3116,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/delimit_fraction", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/filter/delimit_fraction/nextflow.config b/target/nextflow/filter/delimit_fraction/nextflow.config index 97eb6765506..6ca874d63ef 100644 --- a/target/nextflow/filter/delimit_fraction/nextflow.config +++ b/target/nextflow/filter/delimit_fraction/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'filter/delimit_fraction' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Turns a column containing values between 0 and 1 into a boolean column based on thresholds.\n' author = 'Dries Schaumont' } diff --git a/target/nextflow/filter/do_filter/.config.vsh.yaml b/target/nextflow/filter/do_filter/.config.vsh.yaml index 9dadffb83c2..5c58ff223e2 100644 --- a/target/nextflow/filter/do_filter/.config.vsh.yaml +++ b/target/nextflow/filter/do_filter/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "do_filter" namespace: "filter" - version: "1.0.1" + version: "1.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -206,6 +206,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/do_filter" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/do_filter/do_filter" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/filter/do_filter/main.nf b/target/nextflow/filter/do_filter/main.nf index 14c9de494b3..1c6f9551f3f 100644 --- a/target/nextflow/filter/do_filter/main.nf +++ b/target/nextflow/filter/do_filter/main.nf @@ -1,4 +1,4 @@ -// do_filter 1.0.1 +// do_filter 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "do_filter", "namespace" : "filter", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -3053,9 +3053,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/do_filter", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/filter/do_filter/nextflow.config b/target/nextflow/filter/do_filter/nextflow.config index b86caa741ec..2e3be04270a 100644 --- a/target/nextflow/filter/do_filter/nextflow.config +++ b/target/nextflow/filter/do_filter/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'filter/do_filter' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Remove observations and variables based on specified .obs and .var columns.\n' author = 'Robrecht Cannoodt' } diff --git a/target/nextflow/filter/filter_with_counts/.config.vsh.yaml b/target/nextflow/filter/filter_with_counts/.config.vsh.yaml index 8359ca085c5..bd936ed2f57 100644 --- a/target/nextflow/filter/filter_with_counts/.config.vsh.yaml +++ b/target/nextflow/filter/filter_with_counts/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "filter_with_counts" namespace: "filter" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries De Maeyer" roles: @@ -299,6 +299,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/filter_with_counts" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/filter_with_counts/filter_with_counts" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/filter/filter_with_counts/main.nf b/target/nextflow/filter/filter_with_counts/main.nf index e951699696e..17905c1c106 100644 --- a/target/nextflow/filter/filter_with_counts/main.nf +++ b/target/nextflow/filter/filter_with_counts/main.nf @@ -1,4 +1,4 @@ -// filter_with_counts 1.0.1 +// filter_with_counts 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2786,7 +2786,7 @@ meta = [ "functionality" : { "name" : "filter_with_counts", "namespace" : "filter", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries De Maeyer", @@ -3174,9 +3174,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/filter_with_counts", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/filter/filter_with_counts/nextflow.config b/target/nextflow/filter/filter_with_counts/nextflow.config index 080d6a14d94..6d9be985747 100644 --- a/target/nextflow/filter/filter_with_counts/nextflow.config +++ b/target/nextflow/filter/filter_with_counts/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'filter/filter_with_counts' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Filter scRNA-seq data based on the primary QC metrics. \nThis is based on both the UMI counts, the gene counts \nand the mitochondrial genes (genes starting with mt/MT).\n' author = 'Dries De Maeyer, Robrecht Cannoodt' } diff --git a/target/nextflow/filter/filter_with_hvg/.config.vsh.yaml b/target/nextflow/filter/filter_with_hvg/.config.vsh.yaml index e4d6613a941..cd0fa6a7ea7 100644 --- a/target/nextflow/filter/filter_with_hvg/.config.vsh.yaml +++ b/target/nextflow/filter/filter_with_hvg/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "filter_with_hvg" namespace: "filter" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries De Maeyer" roles: @@ -357,6 +357,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/filter_with_hvg" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/filter_with_hvg/filter_with_hvg" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/filter/filter_with_hvg/main.nf b/target/nextflow/filter/filter_with_hvg/main.nf index f121982fa40..060a5d5b3b2 100644 --- a/target/nextflow/filter/filter_with_hvg/main.nf +++ b/target/nextflow/filter/filter_with_hvg/main.nf @@ -1,4 +1,4 @@ -// filter_with_hvg 1.0.1 +// filter_with_hvg 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2786,7 +2786,7 @@ meta = [ "functionality" : { "name" : "filter_with_hvg", "namespace" : "filter", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries De Maeyer", @@ -3201,9 +3201,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/filter_with_hvg", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/filter/filter_with_hvg/nextflow.config b/target/nextflow/filter/filter_with_hvg/nextflow.config index ec65353ceed..3bb2933b9ee 100644 --- a/target/nextflow/filter/filter_with_hvg/nextflow.config +++ b/target/nextflow/filter/filter_with_hvg/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'filter/filter_with_hvg' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Annotate highly variable genes [Satija15] [Zheng17] [Stuart19].\n\nExpects logarithmized data, except when flavor=\'seurat_v3\' in which count data is expected.\n\nDepending on flavor, this reproduces the R-implementations of Seurat [Satija15], Cell Ranger [Zheng17], and Seurat v3 [Stuart19].\n\nFor the dispersion-based methods ([Satija15] and [Zheng17]), the normalized dispersion is obtained by scaling with the mean and standard deviation of the dispersions for genes falling into a given bin for mean expression of genes. This means that for each bin of mean expression, highly variable genes are selected.\n\nFor [Stuart19], a normalized variance for each gene is computed. First, the data are standardized (i.e., z-score normalization per feature) with a regularized standard deviation. Next, the normalized variance is computed as the variance of each gene after the transformation. Genes are ranked by the normalized variance.\n' author = 'Dries De Maeyer, Robrecht Cannoodt' } diff --git a/target/nextflow/filter/filter_with_scrublet/.config.vsh.yaml b/target/nextflow/filter/filter_with_scrublet/.config.vsh.yaml index f549a6349d0..a661d35b23e 100644 --- a/target/nextflow/filter/filter_with_scrublet/.config.vsh.yaml +++ b/target/nextflow/filter/filter_with_scrublet/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "filter_with_scrublet" namespace: "filter" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries De Maeyer" roles: @@ -319,6 +319,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/filter_with_scrublet" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/filter_with_scrublet/filter_with_scrublet" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/filter/filter_with_scrublet/main.nf b/target/nextflow/filter/filter_with_scrublet/main.nf index eb4100b8329..dda17ad27b0 100644 --- a/target/nextflow/filter/filter_with_scrublet/main.nf +++ b/target/nextflow/filter/filter_with_scrublet/main.nf @@ -1,4 +1,4 @@ -// filter_with_scrublet 1.0.1 +// filter_with_scrublet 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2786,7 +2786,7 @@ meta = [ "functionality" : { "name" : "filter_with_scrublet", "namespace" : "filter", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries De Maeyer", @@ -3172,9 +3172,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/filter_with_scrublet", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/filter/filter_with_scrublet/nextflow.config b/target/nextflow/filter/filter_with_scrublet/nextflow.config index 3e67e663432..c5f998215bb 100644 --- a/target/nextflow/filter/filter_with_scrublet/nextflow.config +++ b/target/nextflow/filter/filter_with_scrublet/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'filter/filter_with_scrublet' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Doublet detection using the Scrublet method (Wolock, Lopez and Klein, 2019).\nThe method tests for potential doublets by using the expression profiles of\ncells to generate synthetic potential doubles which are tested against cells. \nThe method returns a "doublet score" on which it calls for potential doublets.\n\nFor the source code please visit https://github.com/AllonKleinLab/scrublet.\n\nFor 10x we expect the doublet rates to be:\n Multiplet Rate (%) - # of Cells Loaded - # of Cells Recovered\n ~0.4% ~800 ~500\n ~0.8% ~1,600 ~1,000\n ~1.6% ~3,200 ~2,000\n ~2.3% ~4,800 ~3,000\n ~3.1% ~6,400 ~4,000\n ~3.9% ~8,000 ~5,000\n ~4.6% ~9,600 ~6,000\n ~5.4% ~11,200 ~7,000\n ~6.1% ~12,800 ~8,000\n ~6.9% ~14,400 ~9,000\n ~7.6% ~16,000 ~10,000\n' author = 'Dries De Maeyer, Robrecht Cannoodt' } diff --git a/target/nextflow/filter/intersect_obs/.config.vsh.yaml b/target/nextflow/filter/intersect_obs/.config.vsh.yaml index 887d4dde4a4..5af5f0a0072 100644 --- a/target/nextflow/filter/intersect_obs/.config.vsh.yaml +++ b/target/nextflow/filter/intersect_obs/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "intersect_obs" namespace: "filter" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -193,6 +193,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/intersect_obs" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/intersect_obs/intersect_obs" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/filter/intersect_obs/main.nf b/target/nextflow/filter/intersect_obs/main.nf index 01e4b5a440e..32f7af32aed 100644 --- a/target/nextflow/filter/intersect_obs/main.nf +++ b/target/nextflow/filter/intersect_obs/main.nf @@ -1,4 +1,4 @@ -// intersect_obs 1.0.1 +// intersect_obs 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2786,7 +2786,7 @@ meta = [ "functionality" : { "name" : "intersect_obs", "namespace" : "filter", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3043,9 +3043,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/intersect_obs", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/filter/intersect_obs/nextflow.config b/target/nextflow/filter/intersect_obs/nextflow.config index 7bad76b5e5a..cfb8c891bdc 100644 --- a/target/nextflow/filter/intersect_obs/nextflow.config +++ b/target/nextflow/filter/intersect_obs/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'filter/intersect_obs' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Create an intersection between two or more modalities.\n\nThis component removes any observations which are not present in all modalities.\n' author = 'Dries Schaumont, Isabelle Bergiers' } diff --git a/target/nextflow/filter/remove_modality/.config.vsh.yaml b/target/nextflow/filter/remove_modality/.config.vsh.yaml index 0a8e3ba56c5..d99a835dccc 100644 --- a/target/nextflow/filter/remove_modality/.config.vsh.yaml +++ b/target/nextflow/filter/remove_modality/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "remove_modality" namespace: "filter" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -175,6 +175,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/remove_modality" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/remove_modality/remove_modality" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/filter/remove_modality/main.nf b/target/nextflow/filter/remove_modality/main.nf index 0f8b289a46a..52c1d33daa6 100644 --- a/target/nextflow/filter/remove_modality/main.nf +++ b/target/nextflow/filter/remove_modality/main.nf @@ -1,4 +1,4 @@ -// remove_modality 1.0.1 +// remove_modality 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "remove_modality", "namespace" : "filter", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3013,9 +3013,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/remove_modality", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/filter/remove_modality/nextflow.config b/target/nextflow/filter/remove_modality/nextflow.config index c0f40b39531..498f8180c43 100644 --- a/target/nextflow/filter/remove_modality/nextflow.config +++ b/target/nextflow/filter/remove_modality/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'filter/remove_modality' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Remove a modality from a .h5mu file\n' author = 'Dries Schaumont' } diff --git a/target/nextflow/filter/subset_h5mu/.config.vsh.yaml b/target/nextflow/filter/subset_h5mu/.config.vsh.yaml index f99062c9de2..06a290e0661 100644 --- a/target/nextflow/filter/subset_h5mu/.config.vsh.yaml +++ b/target/nextflow/filter/subset_h5mu/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "subset_h5mu" namespace: "filter" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -191,6 +191,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/subset_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/subset_h5mu/subset_h5mu" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/filter/subset_h5mu/main.nf b/target/nextflow/filter/subset_h5mu/main.nf index 104262dd55a..ab516868e46 100644 --- a/target/nextflow/filter/subset_h5mu/main.nf +++ b/target/nextflow/filter/subset_h5mu/main.nf @@ -1,4 +1,4 @@ -// subset_h5mu 1.0.1 +// subset_h5mu 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "subset_h5mu", "namespace" : "filter", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3034,9 +3034,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/subset_h5mu", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/filter/subset_h5mu/nextflow.config b/target/nextflow/filter/subset_h5mu/nextflow.config index d340dd420df..abf1239e057 100644 --- a/target/nextflow/filter/subset_h5mu/nextflow.config +++ b/target/nextflow/filter/subset_h5mu/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'filter/subset_h5mu' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Create a subset of a mudata file by selecting the first number of observations\n' author = 'Dries Schaumont' } diff --git a/target/nextflow/genetic_demux/bcftools/.config.vsh.yaml b/target/nextflow/genetic_demux/bcftools/.config.vsh.yaml index bb828d5a624..b509266e803 100644 --- a/target/nextflow/genetic_demux/bcftools/.config.vsh.yaml +++ b/target/nextflow/genetic_demux/bcftools/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "bcftools" namespace: "genetic_demux" - version: "1.0.1" + version: "1.0.2" authors: - name: "Xichen Wu" roles: @@ -179,6 +179,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/genetic_demux/bcftools" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/genetic_demux/bcftools/bcftools" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/genetic_demux/bcftools/main.nf b/target/nextflow/genetic_demux/bcftools/main.nf index 16555e9754c..9a033e267ab 100644 --- a/target/nextflow/genetic_demux/bcftools/main.nf +++ b/target/nextflow/genetic_demux/bcftools/main.nf @@ -1,4 +1,4 @@ -// bcftools 1.0.1 +// bcftools 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "bcftools", "namespace" : "genetic_demux", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Xichen Wu", @@ -3009,9 +3009,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/genetic_demux/bcftools", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/genetic_demux/bcftools/nextflow.config b/target/nextflow/genetic_demux/bcftools/nextflow.config index d94350b06aa..395f1c4f717 100644 --- a/target/nextflow/genetic_demux/bcftools/nextflow.config +++ b/target/nextflow/genetic_demux/bcftools/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'genetic_demux/bcftools' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Filter the variants called by freebayes or cellSNP' author = 'Xichen Wu' } diff --git a/target/nextflow/genetic_demux/cellsnp/.config.vsh.yaml b/target/nextflow/genetic_demux/cellsnp/.config.vsh.yaml index 4aaed9d3225..5f8bc4dd29e 100644 --- a/target/nextflow/genetic_demux/cellsnp/.config.vsh.yaml +++ b/target/nextflow/genetic_demux/cellsnp/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "cellsnp" namespace: "genetic_demux" - version: "1.0.1" + version: "1.0.2" authors: - name: "Xichen Wu" roles: @@ -374,6 +374,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/genetic_demux/cellsnp" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/genetic_demux/cellsnp/cellsnp" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/genetic_demux/cellsnp/main.nf b/target/nextflow/genetic_demux/cellsnp/main.nf index 4f30314736e..7fe71216625 100644 --- a/target/nextflow/genetic_demux/cellsnp/main.nf +++ b/target/nextflow/genetic_demux/cellsnp/main.nf @@ -1,4 +1,4 @@ -// cellsnp 1.0.1 +// cellsnp 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "cellsnp", "namespace" : "genetic_demux", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Xichen Wu", @@ -3227,9 +3227,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/genetic_demux/cellsnp", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/genetic_demux/cellsnp/nextflow.config b/target/nextflow/genetic_demux/cellsnp/nextflow.config index deb9eb940b5..e651600bd34 100644 --- a/target/nextflow/genetic_demux/cellsnp/nextflow.config +++ b/target/nextflow/genetic_demux/cellsnp/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'genetic_demux/cellsnp' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'cellSNP aims to pileup the expressed alleles in single-cell or bulk RNA-seq data. It can be directly used for donor deconvolution in multiplexed single-cell RNA-seq data, particularly with vireo.' author = 'Xichen Wu' } diff --git a/target/nextflow/genetic_demux/demuxlet/.config.vsh.yaml b/target/nextflow/genetic_demux/demuxlet/.config.vsh.yaml index 78c10542efd..2800f779964 100644 --- a/target/nextflow/genetic_demux/demuxlet/.config.vsh.yaml +++ b/target/nextflow/genetic_demux/demuxlet/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "demuxlet" namespace: "genetic_demux" - version: "1.0.1" + version: "1.0.2" authors: - name: "Xichen Wu" roles: @@ -459,6 +459,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/genetic_demux/demuxlet" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/genetic_demux/demuxlet/demuxlet" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/genetic_demux/demuxlet/main.nf b/target/nextflow/genetic_demux/demuxlet/main.nf index 02a662514c0..d4f7c86a293 100644 --- a/target/nextflow/genetic_demux/demuxlet/main.nf +++ b/target/nextflow/genetic_demux/demuxlet/main.nf @@ -1,4 +1,4 @@ -// demuxlet 1.0.1 +// demuxlet 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "demuxlet", "namespace" : "genetic_demux", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Xichen Wu", @@ -3332,9 +3332,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/genetic_demux/demuxlet", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/genetic_demux/demuxlet/nextflow.config b/target/nextflow/genetic_demux/demuxlet/nextflow.config index e31afc27ef8..1f670c3f219 100644 --- a/target/nextflow/genetic_demux/demuxlet/nextflow.config +++ b/target/nextflow/genetic_demux/demuxlet/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'genetic_demux/demuxlet' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Demuxlet is a software tool to deconvolute sample identity and identify multiplets when\nmultiple samples are pooled by barcoded single cell sequencing. If external genotyping data\nfor each sample is available (e.g. from SNP arrays), demuxlet would be recommended. Be careful\nthat the parameters on the github is not in line with the newest help version.\n' author = 'Xichen Wu' } diff --git a/target/nextflow/genetic_demux/dsc_pileup/.config.vsh.yaml b/target/nextflow/genetic_demux/dsc_pileup/.config.vsh.yaml index 39b809b30d1..65e6956e363 100644 --- a/target/nextflow/genetic_demux/dsc_pileup/.config.vsh.yaml +++ b/target/nextflow/genetic_demux/dsc_pileup/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "dsc_pileup" namespace: "genetic_demux" - version: "1.0.1" + version: "1.0.2" authors: - name: "Xichen Wu" roles: @@ -370,6 +370,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/genetic_demux/dsc_pileup" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/genetic_demux/dsc_pileup/dsc_pileup" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/genetic_demux/dsc_pileup/main.nf b/target/nextflow/genetic_demux/dsc_pileup/main.nf index 4527fa52886..095963e78e8 100644 --- a/target/nextflow/genetic_demux/dsc_pileup/main.nf +++ b/target/nextflow/genetic_demux/dsc_pileup/main.nf @@ -1,4 +1,4 @@ -// dsc_pileup 1.0.1 +// dsc_pileup 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "dsc_pileup", "namespace" : "genetic_demux", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Xichen Wu", @@ -3229,9 +3229,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/genetic_demux/dsc_pileup", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/genetic_demux/dsc_pileup/nextflow.config b/target/nextflow/genetic_demux/dsc_pileup/nextflow.config index 0365082379c..c0ed50922b0 100644 --- a/target/nextflow/genetic_demux/dsc_pileup/nextflow.config +++ b/target/nextflow/genetic_demux/dsc_pileup/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'genetic_demux/dsc_pileup' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Dsc-pileup is a software tool to pileup reads and corresponding base quality \nfor each overlapping SNPs and each barcode. By using pileup files,\nit would allow us to run demuxlet/freemuxlet pretty fast multiple times\nwithout going over the BAM file again.\n' author = 'Xichen Wu' } diff --git a/target/nextflow/genetic_demux/freebayes/.config.vsh.yaml b/target/nextflow/genetic_demux/freebayes/.config.vsh.yaml index cc85a450475..787b0360590 100644 --- a/target/nextflow/genetic_demux/freebayes/.config.vsh.yaml +++ b/target/nextflow/genetic_demux/freebayes/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "freebayes" namespace: "genetic_demux" - version: "1.0.1" + version: "1.0.2" authors: - name: "Xichen Wu" roles: @@ -853,6 +853,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/genetic_demux/freebayes" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/genetic_demux/freebayes/freebayes" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/genetic_demux/freebayes/main.nf b/target/nextflow/genetic_demux/freebayes/main.nf index 611f792da3f..ce5b3473974 100644 --- a/target/nextflow/genetic_demux/freebayes/main.nf +++ b/target/nextflow/genetic_demux/freebayes/main.nf @@ -1,4 +1,4 @@ -// freebayes 1.0.1 +// freebayes 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "freebayes", "namespace" : "genetic_demux", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Xichen Wu", @@ -3721,9 +3721,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/genetic_demux/freebayes", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/genetic_demux/freebayes/nextflow.config b/target/nextflow/genetic_demux/freebayes/nextflow.config index 0648d97354e..33d62a0134c 100644 --- a/target/nextflow/genetic_demux/freebayes/nextflow.config +++ b/target/nextflow/genetic_demux/freebayes/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'genetic_demux/freebayes' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Freebayes is a Bayesian genetic variant detector designed to\nfind small polymorphisms, specifically SNPs.\n' author = 'Xichen Wu' } diff --git a/target/nextflow/genetic_demux/freemuxlet/.config.vsh.yaml b/target/nextflow/genetic_demux/freemuxlet/.config.vsh.yaml index 170e61a537f..d86d1f03555 100644 --- a/target/nextflow/genetic_demux/freemuxlet/.config.vsh.yaml +++ b/target/nextflow/genetic_demux/freemuxlet/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "freemuxlet" namespace: "genetic_demux" - version: "1.0.1" + version: "1.0.2" authors: - name: "Xichen Wu" roles: @@ -367,6 +367,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/genetic_demux/freemuxlet" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/genetic_demux/freemuxlet/freemuxlet" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/genetic_demux/freemuxlet/main.nf b/target/nextflow/genetic_demux/freemuxlet/main.nf index 10633bb0391..43c34574f3f 100644 --- a/target/nextflow/genetic_demux/freemuxlet/main.nf +++ b/target/nextflow/genetic_demux/freemuxlet/main.nf @@ -1,4 +1,4 @@ -// freemuxlet 1.0.1 +// freemuxlet 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "freemuxlet", "namespace" : "genetic_demux", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Xichen Wu", @@ -3230,9 +3230,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/genetic_demux/freemuxlet", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/genetic_demux/freemuxlet/nextflow.config b/target/nextflow/genetic_demux/freemuxlet/nextflow.config index 4b81448bc0c..12e08740a55 100644 --- a/target/nextflow/genetic_demux/freemuxlet/nextflow.config +++ b/target/nextflow/genetic_demux/freemuxlet/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'genetic_demux/freemuxlet' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Freemuxlet is a software tool to deconvolute sample identity and identify multiplets when\nmultiple samples are pooled by barcoded single cell sequencing. If external genotyping\ndata is not available, the genotyping-free version demuxlet, freemuxlet, would be recommended.\n' author = 'Xichen Wu' } diff --git a/target/nextflow/genetic_demux/samtools/.config.vsh.yaml b/target/nextflow/genetic_demux/samtools/.config.vsh.yaml index 3bb49790dfd..1a046a17d04 100644 --- a/target/nextflow/genetic_demux/samtools/.config.vsh.yaml +++ b/target/nextflow/genetic_demux/samtools/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "samtools" namespace: "genetic_demux" - version: "1.0.1" + version: "1.0.2" authors: - name: "Xichen Wu" roles: @@ -154,6 +154,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/genetic_demux/samtools" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/genetic_demux/samtools/samtools" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/genetic_demux/samtools/main.nf b/target/nextflow/genetic_demux/samtools/main.nf index f3b941852fb..25ea078c1fb 100644 --- a/target/nextflow/genetic_demux/samtools/main.nf +++ b/target/nextflow/genetic_demux/samtools/main.nf @@ -1,4 +1,4 @@ -// samtools 1.0.1 +// samtools 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "samtools", "namespace" : "genetic_demux", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Xichen Wu", @@ -2984,9 +2984,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/genetic_demux/samtools", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/genetic_demux/samtools/nextflow.config b/target/nextflow/genetic_demux/samtools/nextflow.config index 6e6b8911804..b82437d9412 100644 --- a/target/nextflow/genetic_demux/samtools/nextflow.config +++ b/target/nextflow/genetic_demux/samtools/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'genetic_demux/samtools' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Filter the BAM according to the instruction of scSplit via Samtools.' author = 'Xichen Wu' } diff --git a/target/nextflow/genetic_demux/scsplit/.config.vsh.yaml b/target/nextflow/genetic_demux/scsplit/.config.vsh.yaml index 1b948ad0b15..c8f0bfaa596 100644 --- a/target/nextflow/genetic_demux/scsplit/.config.vsh.yaml +++ b/target/nextflow/genetic_demux/scsplit/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "scsplit" namespace: "genetic_demux" - version: "1.0.1" + version: "1.0.2" authors: - name: "Xichen Wu" roles: @@ -293,6 +293,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/genetic_demux/scsplit" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/genetic_demux/scsplit/scsplit" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/genetic_demux/scsplit/main.nf b/target/nextflow/genetic_demux/scsplit/main.nf index 01e4cfc7e2a..0c581ce4231 100644 --- a/target/nextflow/genetic_demux/scsplit/main.nf +++ b/target/nextflow/genetic_demux/scsplit/main.nf @@ -1,4 +1,4 @@ -// scsplit 1.0.1 +// scsplit 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "scsplit", "namespace" : "genetic_demux", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Xichen Wu", @@ -3141,9 +3141,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/genetic_demux/scsplit", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/genetic_demux/scsplit/nextflow.config b/target/nextflow/genetic_demux/scsplit/nextflow.config index af31f482789..c3a4054cfc4 100644 --- a/target/nextflow/genetic_demux/scsplit/nextflow.config +++ b/target/nextflow/genetic_demux/scsplit/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'genetic_demux/scsplit' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'scsplit is a genotype-free demultiplexing methode of pooled single-cell RNA-seq, using a hidden state model for identifying genetically distinct samples within a mixed population.' author = 'Xichen Wu' } diff --git a/target/nextflow/genetic_demux/souporcell/.config.vsh.yaml b/target/nextflow/genetic_demux/souporcell/.config.vsh.yaml index 9125ad52081..09f1c2881f5 100644 --- a/target/nextflow/genetic_demux/souporcell/.config.vsh.yaml +++ b/target/nextflow/genetic_demux/souporcell/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "souporcell" namespace: "genetic_demux" - version: "1.0.1" + version: "1.0.2" authors: - name: "Xichen Wu" roles: @@ -282,6 +282,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/genetic_demux/souporcell" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/genetic_demux/souporcell/souporcell" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/genetic_demux/souporcell/main.nf b/target/nextflow/genetic_demux/souporcell/main.nf index f45010a4a07..5a51da46faa 100644 --- a/target/nextflow/genetic_demux/souporcell/main.nf +++ b/target/nextflow/genetic_demux/souporcell/main.nf @@ -1,4 +1,4 @@ -// souporcell 1.0.1 +// souporcell 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "souporcell", "namespace" : "genetic_demux", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Xichen Wu", @@ -3123,9 +3123,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/genetic_demux/souporcell", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/genetic_demux/souporcell/nextflow.config b/target/nextflow/genetic_demux/souporcell/nextflow.config index 364f8aab34d..9271c4836cf 100644 --- a/target/nextflow/genetic_demux/souporcell/nextflow.config +++ b/target/nextflow/genetic_demux/souporcell/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'genetic_demux/souporcell' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'souporcell is a method for clustering mixed-genotype scRNAseq experiments by individual.' author = 'Xichen Wu' } diff --git a/target/nextflow/genetic_demux/vireo/.config.vsh.yaml b/target/nextflow/genetic_demux/vireo/.config.vsh.yaml index 45bff62456a..74335a79dbb 100644 --- a/target/nextflow/genetic_demux/vireo/.config.vsh.yaml +++ b/target/nextflow/genetic_demux/vireo/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "vireo" namespace: "genetic_demux" - version: "1.0.1" + version: "1.0.2" authors: - name: "Xichen Wu" roles: @@ -302,6 +302,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/genetic_demux/vireo" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/genetic_demux/vireo/vireo" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/genetic_demux/vireo/main.nf b/target/nextflow/genetic_demux/vireo/main.nf index 1b933517edb..8e4bb5e7b6d 100644 --- a/target/nextflow/genetic_demux/vireo/main.nf +++ b/target/nextflow/genetic_demux/vireo/main.nf @@ -1,4 +1,4 @@ -// vireo 1.0.1 +// vireo 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "vireo", "namespace" : "genetic_demux", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Xichen Wu", @@ -3154,9 +3154,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/genetic_demux/vireo", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/genetic_demux/vireo/nextflow.config b/target/nextflow/genetic_demux/vireo/nextflow.config index 5ac68a89fa8..8d14403728f 100644 --- a/target/nextflow/genetic_demux/vireo/nextflow.config +++ b/target/nextflow/genetic_demux/vireo/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'genetic_demux/vireo' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Vireo is primarily designed for demultiplexing cells into donors by modelling of expressed alleles.' author = 'Xichen Wu' } diff --git a/target/nextflow/integrate/harmonypy/.config.vsh.yaml b/target/nextflow/integrate/harmonypy/.config.vsh.yaml index 216ea3e6320..db03a62a3c0 100644 --- a/target/nextflow/integrate/harmonypy/.config.vsh.yaml +++ b/target/nextflow/integrate/harmonypy/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "harmonypy" namespace: "integrate" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -245,6 +245,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/integrate/harmonypy" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/integrate/harmonypy/harmonypy" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/integrate/harmonypy/main.nf b/target/nextflow/integrate/harmonypy/main.nf index 6ee64666c4f..eb8d3729e8a 100644 --- a/target/nextflow/integrate/harmonypy/main.nf +++ b/target/nextflow/integrate/harmonypy/main.nf @@ -1,4 +1,4 @@ -// harmonypy 1.0.1 +// harmonypy 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2786,7 +2786,7 @@ meta = [ "functionality" : { "name" : "harmonypy", "namespace" : "integrate", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3100,9 +3100,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/integrate/harmonypy", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/integrate/harmonypy/nextflow.config b/target/nextflow/integrate/harmonypy/nextflow.config index 032fe243016..419aff45197 100644 --- a/target/nextflow/integrate/harmonypy/nextflow.config +++ b/target/nextflow/integrate/harmonypy/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'integrate/harmonypy' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Performs Harmony integration based as described in https://github.com/immunogenomics/harmony. Based on an implementation in python from https://github.com/slowkow/harmonypy' author = 'Dries Schaumont, Robrecht Cannoodt' } diff --git a/target/nextflow/integrate/scanorama/.config.vsh.yaml b/target/nextflow/integrate/scanorama/.config.vsh.yaml index 183ba98db72..c787a235afe 100644 --- a/target/nextflow/integrate/scanorama/.config.vsh.yaml +++ b/target/nextflow/integrate/scanorama/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "scanorama" namespace: "integrate" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries De Maeyer" roles: @@ -288,6 +288,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/integrate/scanorama" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/integrate/scanorama/scanorama" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/integrate/scanorama/main.nf b/target/nextflow/integrate/scanorama/main.nf index 671921957f6..e5ca54cca0f 100644 --- a/target/nextflow/integrate/scanorama/main.nf +++ b/target/nextflow/integrate/scanorama/main.nf @@ -1,4 +1,4 @@ -// scanorama 1.0.1 +// scanorama 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2786,7 +2786,7 @@ meta = [ "functionality" : { "name" : "scanorama", "namespace" : "integrate", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries De Maeyer", @@ -3149,9 +3149,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/integrate/scanorama", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/integrate/scanorama/nextflow.config b/target/nextflow/integrate/scanorama/nextflow.config index 718a4f42d1e..79402957cf2 100644 --- a/target/nextflow/integrate/scanorama/nextflow.config +++ b/target/nextflow/integrate/scanorama/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'integrate/scanorama' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Use Scanorama to integrate different experiments.\n' author = 'Dries De Maeyer, Dries Schaumont' } diff --git a/target/nextflow/integrate/scarches/.config.vsh.yaml b/target/nextflow/integrate/scarches/.config.vsh.yaml index ad52773294e..6607e0050ac 100644 --- a/target/nextflow/integrate/scarches/.config.vsh.yaml +++ b/target/nextflow/integrate/scarches/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "scarches" namespace: "integrate" - version: "1.0.1" + version: "1.0.2" authors: - name: "Vladimir Shitov" info: @@ -336,6 +336,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/integrate/scarches" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/integrate/scarches/scarches" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/integrate/scarches/main.nf b/target/nextflow/integrate/scarches/main.nf index 46d444fe82c..fc476477e57 100644 --- a/target/nextflow/integrate/scarches/main.nf +++ b/target/nextflow/integrate/scarches/main.nf @@ -1,4 +1,4 @@ -// scarches 1.0.1 +// scarches 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "scarches", "namespace" : "integrate", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Vladimir Shitov", @@ -3206,9 +3206,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/integrate/scarches", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/integrate/scarches/nextflow.config b/target/nextflow/integrate/scarches/nextflow.config index 343e8f5a3b3..d003d184da8 100644 --- a/target/nextflow/integrate/scarches/nextflow.config +++ b/target/nextflow/integrate/scarches/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'integrate/scarches' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Performs reference mapping with scArches' author = 'Vladimir Shitov' } diff --git a/target/nextflow/integrate/scvi/.config.vsh.yaml b/target/nextflow/integrate/scvi/.config.vsh.yaml index a3cb65d0391..d9aed4ad58b 100644 --- a/target/nextflow/integrate/scvi/.config.vsh.yaml +++ b/target/nextflow/integrate/scvi/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "scvi" namespace: "integrate" - version: "1.0.1" + version: "1.0.2" authors: - name: "Malte D. Luecken" roles: @@ -594,6 +594,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/integrate/scvi" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/integrate/scvi/scvi" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/integrate/scvi/main.nf b/target/nextflow/integrate/scvi/main.nf index 625bd537eb5..67af3546477 100644 --- a/target/nextflow/integrate/scvi/main.nf +++ b/target/nextflow/integrate/scvi/main.nf @@ -1,4 +1,4 @@ -// scvi 1.0.1 +// scvi 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2787,7 +2787,7 @@ meta = [ "functionality" : { "name" : "scvi", "namespace" : "integrate", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Malte D. Luecken", @@ -3506,9 +3506,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/integrate/scvi", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/integrate/scvi/nextflow.config b/target/nextflow/integrate/scvi/nextflow.config index 7f7a3cbee57..704bc7eb734 100644 --- a/target/nextflow/integrate/scvi/nextflow.config +++ b/target/nextflow/integrate/scvi/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'integrate/scvi' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Performs scvi integration as done in the human lung cell atlas https://github.com/LungCellAtlas/HLCA' author = 'Malte D. Luecken, Dries Schaumont, Matthias Beyens' } diff --git a/target/nextflow/integrate/totalvi/.config.vsh.yaml b/target/nextflow/integrate/totalvi/.config.vsh.yaml index cfd4fdbacaa..964830ead2b 100644 --- a/target/nextflow/integrate/totalvi/.config.vsh.yaml +++ b/target/nextflow/integrate/totalvi/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "totalvi" namespace: "integrate" - version: "1.0.1" + version: "1.0.2" authors: - name: "Vladimir Shitov" info: @@ -353,6 +353,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/integrate/totalvi" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/integrate/totalvi/totalvi" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/integrate/totalvi/main.nf b/target/nextflow/integrate/totalvi/main.nf index 973d2d2ec47..22ea07a2e29 100644 --- a/target/nextflow/integrate/totalvi/main.nf +++ b/target/nextflow/integrate/totalvi/main.nf @@ -1,4 +1,4 @@ -// totalvi 1.0.1 +// totalvi 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "totalvi", "namespace" : "integrate", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Vladimir Shitov", @@ -3226,9 +3226,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/integrate/totalvi", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/integrate/totalvi/nextflow.config b/target/nextflow/integrate/totalvi/nextflow.config index 7bc37dba3c8..942b7131ec0 100644 --- a/target/nextflow/integrate/totalvi/nextflow.config +++ b/target/nextflow/integrate/totalvi/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'integrate/totalvi' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Performs mapping to the reference by totalvi model: https://docs.scvi-tools.org/en/stable/tutorials/notebooks/scarches_scvi_tools.html#Reference-mapping-with-TOTALVI' author = 'Vladimir Shitov' } diff --git a/target/nextflow/interpret/lianapy/.config.vsh.yaml b/target/nextflow/interpret/lianapy/.config.vsh.yaml index 07c80124ea1..97f6a019969 100644 --- a/target/nextflow/interpret/lianapy/.config.vsh.yaml +++ b/target/nextflow/interpret/lianapy/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "lianapy" namespace: "interpret" - version: "1.0.1" + version: "1.0.2" authors: - name: "Mauro Saporita" roles: @@ -317,6 +317,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/interpret/lianapy" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/interpret/lianapy/lianapy" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/interpret/lianapy/main.nf b/target/nextflow/interpret/lianapy/main.nf index e96b943a304..eae655523b9 100644 --- a/target/nextflow/interpret/lianapy/main.nf +++ b/target/nextflow/interpret/lianapy/main.nf @@ -1,4 +1,4 @@ -// lianapy 1.0.1 +// lianapy 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2786,7 +2786,7 @@ meta = [ "functionality" : { "name" : "lianapy", "namespace" : "interpret", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Mauro Saporita", @@ -3176,9 +3176,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/interpret/lianapy", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/interpret/lianapy/nextflow.config b/target/nextflow/interpret/lianapy/nextflow.config index 9e60cc6caa6..9425e6d642f 100644 --- a/target/nextflow/interpret/lianapy/nextflow.config +++ b/target/nextflow/interpret/lianapy/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'interpret/lianapy' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Performs LIANA integration based as described in https://github.com/saezlab/liana-py' author = 'Mauro Saporita, Povilas Gibas' } diff --git a/target/nextflow/labels_transfer/knn/.config.vsh.yaml b/target/nextflow/labels_transfer/knn/.config.vsh.yaml index 31ea561e2e6..012dc469a2c 100644 --- a/target/nextflow/labels_transfer/knn/.config.vsh.yaml +++ b/target/nextflow/labels_transfer/knn/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "knn" namespace: "labels_transfer" - version: "1.0.1" + version: "1.0.2" authors: - name: "Vladimir Shitov" roles: @@ -384,6 +384,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/labels_transfer/knn" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/labels_transfer/knn/knn" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/labels_transfer/knn/main.nf b/target/nextflow/labels_transfer/knn/main.nf index 6c1c49ed37b..3e65477d8aa 100644 --- a/target/nextflow/labels_transfer/knn/main.nf +++ b/target/nextflow/labels_transfer/knn/main.nf @@ -1,4 +1,4 @@ -// knn 1.0.1 +// knn 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "knn", "namespace" : "labels_transfer", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Vladimir Shitov", @@ -3273,9 +3273,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/labels_transfer/knn", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/labels_transfer/knn/nextflow.config b/target/nextflow/labels_transfer/knn/nextflow.config index 002b8228f91..62cd846f928 100644 --- a/target/nextflow/labels_transfer/knn/nextflow.config +++ b/target/nextflow/labels_transfer/knn/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'labels_transfer/knn' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Performs label transfer from reference to query using KNN classifier' author = 'Vladimir Shitov' } diff --git a/target/nextflow/labels_transfer/xgboost/.config.vsh.yaml b/target/nextflow/labels_transfer/xgboost/.config.vsh.yaml index 2c6776e937c..b1900372859 100644 --- a/target/nextflow/labels_transfer/xgboost/.config.vsh.yaml +++ b/target/nextflow/labels_transfer/xgboost/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "xgboost" namespace: "labels_transfer" - version: "1.0.1" + version: "1.0.2" authors: - name: "Vladimir Shitov" roles: @@ -599,6 +599,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/labels_transfer/xgboost" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/labels_transfer/xgboost/xgboost" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/labels_transfer/xgboost/main.nf b/target/nextflow/labels_transfer/xgboost/main.nf index a07905ff471..b5c9a4667a0 100644 --- a/target/nextflow/labels_transfer/xgboost/main.nf +++ b/target/nextflow/labels_transfer/xgboost/main.nf @@ -1,4 +1,4 @@ -// xgboost 1.0.1 +// xgboost 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "xgboost", "namespace" : "labels_transfer", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Vladimir Shitov", @@ -3509,9 +3509,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/labels_transfer/xgboost", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/labels_transfer/xgboost/nextflow.config b/target/nextflow/labels_transfer/xgboost/nextflow.config index 4419198a1f2..a7299fa0a2c 100644 --- a/target/nextflow/labels_transfer/xgboost/nextflow.config +++ b/target/nextflow/labels_transfer/xgboost/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'labels_transfer/xgboost' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Performs label transfer from reference to query using XGBoost classifier' author = 'Vladimir Shitov' } diff --git a/target/nextflow/mapping/bd_rhapsody/.config.vsh.yaml b/target/nextflow/mapping/bd_rhapsody/.config.vsh.yaml index dcf3ce0c169..2daa51dbeb5 100644 --- a/target/nextflow/mapping/bd_rhapsody/.config.vsh.yaml +++ b/target/nextflow/mapping/bd_rhapsody/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "bd_rhapsody" namespace: "mapping" - version: "1.0.1" + version: "1.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -420,6 +420,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/bd_rhapsody" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/bd_rhapsody/bd_rhapsody" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/mapping/bd_rhapsody/main.nf b/target/nextflow/mapping/bd_rhapsody/main.nf index 3324b8f61c1..882ae304385 100644 --- a/target/nextflow/mapping/bd_rhapsody/main.nf +++ b/target/nextflow/mapping/bd_rhapsody/main.nf @@ -1,4 +1,4 @@ -// bd_rhapsody 1.0.1 +// bd_rhapsody 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "bd_rhapsody", "namespace" : "mapping", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -3303,9 +3303,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/bd_rhapsody", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/mapping/bd_rhapsody/nextflow.config b/target/nextflow/mapping/bd_rhapsody/nextflow.config index 8625baea6b2..a518328fdee 100644 --- a/target/nextflow/mapping/bd_rhapsody/nextflow.config +++ b/target/nextflow/mapping/bd_rhapsody/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'mapping/bd_rhapsody' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'A wrapper for the BD Rhapsody Analysis CWL v1.10.1 pipeline.\n\nThe CWL pipeline file is obtained by cloning \'https://bitbucket.org/CRSwDev/cwl/src/master/\' and removing all objects with class \'DockerRequirement\' from the YML.\n\nThis pipeline can be used for a targeted analysis (with `--mode targeted`) or for a whole transcriptome analysis (with `--mode wta`).\n\n* If mode is `"targeted"`, then either the `--reference` or `--abseq_reference` parameters must be defined.\n* If mode is `"wta"`, then `--reference` and `--transcriptome_annotation` must be defined, `--abseq_reference` and `--supplemental_reference` is optional.\n\nThe reference_genome and transcriptome_annotation files can be generated with the make_reference pipeline.\nAlternatively, BD also provides standard references which can be downloaded from these locations:\n\n - Human: http://bd-rhapsody-public.s3-website-us-east-1.amazonaws.com/Rhapsody-WTA/GRCh38-PhiX-gencodev29/\n - Mouse: http://bd-rhapsody-public.s3-website-us-east-1.amazonaws.com/Rhapsody-WTA/GRCm38-PhiX-gencodevM19/\n' author = 'Robrecht Cannoodt' } diff --git a/target/nextflow/mapping/cellranger_count/.config.vsh.yaml b/target/nextflow/mapping/cellranger_count/.config.vsh.yaml index afe1f8e991e..98aa741b264 100644 --- a/target/nextflow/mapping/cellranger_count/.config.vsh.yaml +++ b/target/nextflow/mapping/cellranger_count/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "cellranger_count" namespace: "mapping" - version: "1.0.1" + version: "1.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -270,6 +270,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/cellranger_count" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/cellranger_count/cellranger_count" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/mapping/cellranger_count/main.nf b/target/nextflow/mapping/cellranger_count/main.nf index 07835c47ff8..09c1de962f6 100644 --- a/target/nextflow/mapping/cellranger_count/main.nf +++ b/target/nextflow/mapping/cellranger_count/main.nf @@ -1,4 +1,4 @@ -// cellranger_count 1.0.1 +// cellranger_count 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2787,7 +2787,7 @@ meta = [ "functionality" : { "name" : "cellranger_count", "namespace" : "mapping", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Angela Oliveira Pisco", @@ -3134,9 +3134,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/cellranger_count", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/mapping/cellranger_count/nextflow.config b/target/nextflow/mapping/cellranger_count/nextflow.config index 93c45682db0..19e64d3d8ab 100644 --- a/target/nextflow/mapping/cellranger_count/nextflow.config +++ b/target/nextflow/mapping/cellranger_count/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'mapping/cellranger_count' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Align fastq files using Cell Ranger count.' author = 'Angela Oliveira Pisco, Samuel D\'Souza, Robrecht Cannoodt' } diff --git a/target/nextflow/mapping/cellranger_count_split/.config.vsh.yaml b/target/nextflow/mapping/cellranger_count_split/.config.vsh.yaml index 18bf30e86bc..c68231e14a9 100644 --- a/target/nextflow/mapping/cellranger_count_split/.config.vsh.yaml +++ b/target/nextflow/mapping/cellranger_count_split/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "cellranger_count_split" namespace: "mapping" - version: "1.0.1" + version: "1.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -222,6 +222,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/cellranger_count_split" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/cellranger_count_split/cellranger_count_split" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/mapping/cellranger_count_split/main.nf b/target/nextflow/mapping/cellranger_count_split/main.nf index b23549ed7f5..cb2f3d91415 100644 --- a/target/nextflow/mapping/cellranger_count_split/main.nf +++ b/target/nextflow/mapping/cellranger_count_split/main.nf @@ -1,4 +1,4 @@ -// cellranger_count_split 1.0.1 +// cellranger_count_split 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2787,7 +2787,7 @@ meta = [ "functionality" : { "name" : "cellranger_count_split", "namespace" : "mapping", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Angela Oliveira Pisco", @@ -3074,9 +3074,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/cellranger_count_split", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/mapping/cellranger_count_split/nextflow.config b/target/nextflow/mapping/cellranger_count_split/nextflow.config index af775c63d29..85be1021bbc 100644 --- a/target/nextflow/mapping/cellranger_count_split/nextflow.config +++ b/target/nextflow/mapping/cellranger_count_split/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'mapping/cellranger_count_split' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Split 10x Cell Ranger output directory into separate output fields.' author = 'Angela Oliveira Pisco, Samuel D\'Souza, Robrecht Cannoodt' } diff --git a/target/nextflow/mapping/cellranger_multi/.config.vsh.yaml b/target/nextflow/mapping/cellranger_multi/.config.vsh.yaml index e5b3a60e4e7..5bd2c9d2ff7 100644 --- a/target/nextflow/mapping/cellranger_multi/.config.vsh.yaml +++ b/target/nextflow/mapping/cellranger_multi/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "cellranger_multi" namespace: "mapping" - version: "1.0.1" + version: "1.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -585,6 +585,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/cellranger_multi" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/cellranger_multi/cellranger_multi" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/mapping/cellranger_multi/main.nf b/target/nextflow/mapping/cellranger_multi/main.nf index a1ba1318b50..24daa986a3d 100644 --- a/target/nextflow/mapping/cellranger_multi/main.nf +++ b/target/nextflow/mapping/cellranger_multi/main.nf @@ -1,4 +1,4 @@ -// cellranger_multi 1.0.1 +// cellranger_multi 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2787,7 +2787,7 @@ meta = [ "functionality" : { "name" : "cellranger_multi", "namespace" : "mapping", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Angela Oliveira Pisco", @@ -3481,9 +3481,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/cellranger_multi", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/mapping/cellranger_multi/nextflow.config b/target/nextflow/mapping/cellranger_multi/nextflow.config index 1c01b1c6730..7f535c472b2 100644 --- a/target/nextflow/mapping/cellranger_multi/nextflow.config +++ b/target/nextflow/mapping/cellranger_multi/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'mapping/cellranger_multi' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Align fastq files using Cell Ranger multi.' author = 'Angela Oliveira Pisco, Robrecht Cannoodt, Dries De Maeyer' } diff --git a/target/nextflow/mapping/htseq_count/.config.vsh.yaml b/target/nextflow/mapping/htseq_count/.config.vsh.yaml index 0ad516cfb15..fdb7cc6cfe2 100644 --- a/target/nextflow/mapping/htseq_count/.config.vsh.yaml +++ b/target/nextflow/mapping/htseq_count/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "htseq_count" namespace: "mapping" - version: "1.0.1" + version: "1.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -421,6 +421,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/htseq_count" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/htseq_count/htseq_count" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/mapping/htseq_count/main.nf b/target/nextflow/mapping/htseq_count/main.nf index 7822fb8353e..d0283d50c07 100644 --- a/target/nextflow/mapping/htseq_count/main.nf +++ b/target/nextflow/mapping/htseq_count/main.nf @@ -1,4 +1,4 @@ -// htseq_count 1.0.1 +// htseq_count 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2786,7 +2786,7 @@ meta = [ "functionality" : { "name" : "htseq_count", "namespace" : "mapping", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -3324,9 +3324,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/htseq_count", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/mapping/htseq_count/nextflow.config b/target/nextflow/mapping/htseq_count/nextflow.config index 2fdd3d39774..5f627daac1f 100644 --- a/target/nextflow/mapping/htseq_count/nextflow.config +++ b/target/nextflow/mapping/htseq_count/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'mapping/htseq_count' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Quantify gene expression for subsequent testing for differential expression.\n\nThis script takes one or more alignment files in SAM/BAM format and a feature file in GFF format and calculates for each feature the number of reads mapping to it. \n\nSee http://htseq.readthedocs.io/en/master/count.html for details.\n' author = 'Robrecht Cannoodt, Angela Oliveira Pisco' } diff --git a/target/nextflow/mapping/htseq_count_to_h5mu/.config.vsh.yaml b/target/nextflow/mapping/htseq_count_to_h5mu/.config.vsh.yaml index 6211ba5b3fe..fb1a35332c0 100644 --- a/target/nextflow/mapping/htseq_count_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/mapping/htseq_count_to_h5mu/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "htseq_count_to_h5mu" namespace: "mapping" - version: "1.0.1" + version: "1.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -213,6 +213,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/htseq_count_to_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/htseq_count_to_h5mu/htseq_count_to_h5mu" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/mapping/htseq_count_to_h5mu/main.nf b/target/nextflow/mapping/htseq_count_to_h5mu/main.nf index 578a109ac49..6dc88d71f13 100644 --- a/target/nextflow/mapping/htseq_count_to_h5mu/main.nf +++ b/target/nextflow/mapping/htseq_count_to_h5mu/main.nf @@ -1,4 +1,4 @@ -// htseq_count_to_h5mu 1.0.1 +// htseq_count_to_h5mu 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2786,7 +2786,7 @@ meta = [ "functionality" : { "name" : "htseq_count_to_h5mu", "namespace" : "mapping", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -3070,9 +3070,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/htseq_count_to_h5mu", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/mapping/htseq_count_to_h5mu/nextflow.config b/target/nextflow/mapping/htseq_count_to_h5mu/nextflow.config index c752e2b1042..3121136025c 100644 --- a/target/nextflow/mapping/htseq_count_to_h5mu/nextflow.config +++ b/target/nextflow/mapping/htseq_count_to_h5mu/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'mapping/htseq_count_to_h5mu' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Convert the htseq table to a h5mu.\n' author = 'Robrecht Cannoodt, Angela Oliveira Pisco' } diff --git a/target/nextflow/mapping/multi_star/.config.vsh.yaml b/target/nextflow/mapping/multi_star/.config.vsh.yaml index 906ef70b637..34356d24b6d 100644 --- a/target/nextflow/mapping/multi_star/.config.vsh.yaml +++ b/target/nextflow/mapping/multi_star/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "multi_star" namespace: "mapping" - version: "1.0.1" + version: "1.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -3083,6 +3083,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/multi_star" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/multi_star/multi_star" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/mapping/multi_star/main.nf b/target/nextflow/mapping/multi_star/main.nf index 6bb21e9dad4..d44a6b28877 100644 --- a/target/nextflow/mapping/multi_star/main.nf +++ b/target/nextflow/mapping/multi_star/main.nf @@ -1,4 +1,4 @@ -// multi_star 1.0.1 +// multi_star 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2786,7 +2786,7 @@ meta = [ "functionality" : { "name" : "multi_star", "namespace" : "mapping", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Angela Oliveira Pisco", @@ -6366,9 +6366,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/multi_star", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/mapping/multi_star/nextflow.config b/target/nextflow/mapping/multi_star/nextflow.config index 3521b2471a0..98e948afe6a 100644 --- a/target/nextflow/mapping/multi_star/nextflow.config +++ b/target/nextflow/mapping/multi_star/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'mapping/multi_star' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Align fastq files using STAR.' author = 'Angela Oliveira Pisco, Robrecht Cannoodt' } diff --git a/target/nextflow/mapping/multi_star_to_h5mu/.config.vsh.yaml b/target/nextflow/mapping/multi_star_to_h5mu/.config.vsh.yaml index c5926240d0c..277041613f9 100644 --- a/target/nextflow/mapping/multi_star_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/mapping/multi_star_to_h5mu/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "multi_star_to_h5mu" namespace: "mapping" - version: "1.0.1" + version: "1.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -183,6 +183,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/multi_star_to_h5mu" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/multi_star_to_h5mu/multi_star_to_h5mu" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/mapping/multi_star_to_h5mu/main.nf b/target/nextflow/mapping/multi_star_to_h5mu/main.nf index aea531a987e..474fc14933a 100644 --- a/target/nextflow/mapping/multi_star_to_h5mu/main.nf +++ b/target/nextflow/mapping/multi_star_to_h5mu/main.nf @@ -1,4 +1,4 @@ -// multi_star_to_h5mu 1.0.1 +// multi_star_to_h5mu 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2786,7 +2786,7 @@ meta = [ "functionality" : { "name" : "multi_star_to_h5mu", "namespace" : "mapping", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -3030,9 +3030,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/multi_star_to_h5mu", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/mapping/multi_star_to_h5mu/nextflow.config b/target/nextflow/mapping/multi_star_to_h5mu/nextflow.config index cf9f2112a06..b85c05699fc 100644 --- a/target/nextflow/mapping/multi_star_to_h5mu/nextflow.config +++ b/target/nextflow/mapping/multi_star_to_h5mu/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'mapping/multi_star_to_h5mu' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Convert the output of `multi_star` to a h5mu.\n' author = 'Robrecht Cannoodt, Angela Oliveira Pisco' } diff --git a/target/nextflow/mapping/samtools_sort/.config.vsh.yaml b/target/nextflow/mapping/samtools_sort/.config.vsh.yaml index b9575adfd47..5a24fd321b9 100644 --- a/target/nextflow/mapping/samtools_sort/.config.vsh.yaml +++ b/target/nextflow/mapping/samtools_sort/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "samtools_sort" namespace: "mapping" - version: "1.0.1" + version: "1.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -273,6 +273,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/samtools_sort" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/samtools_sort/samtools_sort" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/mapping/samtools_sort/main.nf b/target/nextflow/mapping/samtools_sort/main.nf index 1bc11249cfb..41c4124eb88 100644 --- a/target/nextflow/mapping/samtools_sort/main.nf +++ b/target/nextflow/mapping/samtools_sort/main.nf @@ -1,4 +1,4 @@ -// samtools_sort 1.0.1 +// samtools_sort 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2786,7 +2786,7 @@ meta = [ "functionality" : { "name" : "samtools_sort", "namespace" : "mapping", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -3141,9 +3141,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/samtools_sort", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/mapping/samtools_sort/nextflow.config b/target/nextflow/mapping/samtools_sort/nextflow.config index 65ffa237b37..860fe8cce61 100644 --- a/target/nextflow/mapping/samtools_sort/nextflow.config +++ b/target/nextflow/mapping/samtools_sort/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'mapping/samtools_sort' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Sort and (optionally) index alignments.\n\nReads are sorted by leftmost coordinates, or by read name when `--sort_by_read_names` is used.\n\nAn appropriate `@HD-SO` sort order header tag will be added or an existing one updated if necessary.\n\nNote that to generate an index file (by specifying `--output_bai`), the default coordinate sort must be used.\nThus the `--sort_by_read_names` and `--sort_by ` options are incompatible with `--output_bai`. \n' author = 'Robrecht Cannoodt, Angela Oliveira Pisco' } diff --git a/target/nextflow/mapping/star_align/.config.vsh.yaml b/target/nextflow/mapping/star_align/.config.vsh.yaml index 9f69b884538..50509392831 100644 --- a/target/nextflow/mapping/star_align/.config.vsh.yaml +++ b/target/nextflow/mapping/star_align/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "star_align" namespace: "mapping" - version: "1.0.1" + version: "1.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -2538,6 +2538,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/star_align" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/star_align/star_align" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/mapping/star_align/main.nf b/target/nextflow/mapping/star_align/main.nf index 521d0ecef37..eecaf585835 100644 --- a/target/nextflow/mapping/star_align/main.nf +++ b/target/nextflow/mapping/star_align/main.nf @@ -1,4 +1,4 @@ -// star_align 1.0.1 +// star_align 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2786,7 +2786,7 @@ meta = [ "functionality" : { "name" : "star_align", "namespace" : "mapping", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Angela Oliveira Pisco", @@ -5415,9 +5415,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/star_align", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/mapping/star_align/nextflow.config b/target/nextflow/mapping/star_align/nextflow.config index fa19b809645..85243f17b1d 100644 --- a/target/nextflow/mapping/star_align/nextflow.config +++ b/target/nextflow/mapping/star_align/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'mapping/star_align' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Align fastq files using STAR.' author = 'Angela Oliveira Pisco, Robrecht Cannoodt' } diff --git a/target/nextflow/mapping/star_align_v273a/.config.vsh.yaml b/target/nextflow/mapping/star_align_v273a/.config.vsh.yaml index 25a90d2e3bb..89f898848fb 100644 --- a/target/nextflow/mapping/star_align_v273a/.config.vsh.yaml +++ b/target/nextflow/mapping/star_align_v273a/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "star_align_v273a" namespace: "mapping" - version: "1.0.1" + version: "1.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -2538,6 +2538,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/star_align_v273a" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/star_align_v273a/star_align_v273a" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/mapping/star_align_v273a/main.nf b/target/nextflow/mapping/star_align_v273a/main.nf index 78b54b7ad11..ffaa5c283ca 100644 --- a/target/nextflow/mapping/star_align_v273a/main.nf +++ b/target/nextflow/mapping/star_align_v273a/main.nf @@ -1,4 +1,4 @@ -// star_align_v273a 1.0.1 +// star_align_v273a 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2786,7 +2786,7 @@ meta = [ "functionality" : { "name" : "star_align_v273a", "namespace" : "mapping", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Angela Oliveira Pisco", @@ -5415,9 +5415,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/star_align_v273a", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/mapping/star_align_v273a/nextflow.config b/target/nextflow/mapping/star_align_v273a/nextflow.config index 46efb4c3b04..7322ec0e764 100644 --- a/target/nextflow/mapping/star_align_v273a/nextflow.config +++ b/target/nextflow/mapping/star_align_v273a/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'mapping/star_align_v273a' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Align fastq files using STAR.' author = 'Angela Oliveira Pisco, Robrecht Cannoodt' } diff --git a/target/nextflow/mapping/star_build_reference/.config.vsh.yaml b/target/nextflow/mapping/star_build_reference/.config.vsh.yaml index 23335c89c98..26dd3230bc7 100644 --- a/target/nextflow/mapping/star_build_reference/.config.vsh.yaml +++ b/target/nextflow/mapping/star_build_reference/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "star_build_reference" namespace: "mapping" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -193,6 +193,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/star_build_reference" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/star_build_reference/star_build_reference" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/mapping/star_build_reference/main.nf b/target/nextflow/mapping/star_build_reference/main.nf index bd7205d5dee..e0b470c0c51 100644 --- a/target/nextflow/mapping/star_build_reference/main.nf +++ b/target/nextflow/mapping/star_build_reference/main.nf @@ -1,4 +1,4 @@ -// star_build_reference 1.0.1 +// star_build_reference 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "star_build_reference", "namespace" : "mapping", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3025,9 +3025,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/star_build_reference", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/mapping/star_build_reference/nextflow.config b/target/nextflow/mapping/star_build_reference/nextflow.config index 9a4725dcd19..275590cb9a7 100644 --- a/target/nextflow/mapping/star_build_reference/nextflow.config +++ b/target/nextflow/mapping/star_build_reference/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'mapping/star_build_reference' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Create a reference for STAR from a set of fasta files.' author = 'Dries Schaumont' } diff --git a/target/nextflow/metadata/add_id/.config.vsh.yaml b/target/nextflow/metadata/add_id/.config.vsh.yaml index 08bdec0ee3f..1167edc7e3b 100644 --- a/target/nextflow/metadata/add_id/.config.vsh.yaml +++ b/target/nextflow/metadata/add_id/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "add_id" namespace: "metadata" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -209,6 +209,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/add_id" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/add_id/add_id" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/metadata/add_id/main.nf b/target/nextflow/metadata/add_id/main.nf index 8a4f90275ab..098427bb92e 100644 --- a/target/nextflow/metadata/add_id/main.nf +++ b/target/nextflow/metadata/add_id/main.nf @@ -1,4 +1,4 @@ -// add_id 1.0.1 +// add_id 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "add_id", "namespace" : "metadata", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3062,9 +3062,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/add_id", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/metadata/add_id/nextflow.config b/target/nextflow/metadata/add_id/nextflow.config index 1959b28adb8..1c6eb22971f 100644 --- a/target/nextflow/metadata/add_id/nextflow.config +++ b/target/nextflow/metadata/add_id/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'metadata/add_id' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Add id of .obs. Also allows to make .obs_names (the .obs index) unique \nby prefixing the values with an unique id per .h5mu file.\n' author = 'Dries Schaumont' } diff --git a/target/nextflow/metadata/grep_annotation_column/.config.vsh.yaml b/target/nextflow/metadata/grep_annotation_column/.config.vsh.yaml index ca34ea0629f..38148736fb1 100644 --- a/target/nextflow/metadata/grep_annotation_column/.config.vsh.yaml +++ b/target/nextflow/metadata/grep_annotation_column/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "grep_annotation_column" namespace: "metadata" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -267,6 +267,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/grep_annotation_column" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/grep_annotation_column/grep_annotation_column" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/metadata/grep_annotation_column/main.nf b/target/nextflow/metadata/grep_annotation_column/main.nf index 26a039ffd8d..acd1095232d 100644 --- a/target/nextflow/metadata/grep_annotation_column/main.nf +++ b/target/nextflow/metadata/grep_annotation_column/main.nf @@ -1,4 +1,4 @@ -// grep_annotation_column 1.0.1 +// grep_annotation_column 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "grep_annotation_column", "namespace" : "metadata", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3128,9 +3128,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/grep_annotation_column", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/metadata/grep_annotation_column/nextflow.config b/target/nextflow/metadata/grep_annotation_column/nextflow.config index faec469aab9..d6d735531cf 100644 --- a/target/nextflow/metadata/grep_annotation_column/nextflow.config +++ b/target/nextflow/metadata/grep_annotation_column/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'metadata/grep_annotation_column' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Perform a regex lookup on a column from the annotation matrices .obs or .var.\nThe annotation matrix can originate from either a modality, or all modalities (global .var or .obs).\n' author = 'Dries Schaumont' } diff --git a/target/nextflow/metadata/join_csv/.config.vsh.yaml b/target/nextflow/metadata/join_csv/.config.vsh.yaml index 4a3544c3d5d..4e36ab4ec0e 100644 --- a/target/nextflow/metadata/join_csv/.config.vsh.yaml +++ b/target/nextflow/metadata/join_csv/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "join_csv" namespace: "metadata" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -241,6 +241,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/join_csv" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/join_csv/join_csv" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/metadata/join_csv/main.nf b/target/nextflow/metadata/join_csv/main.nf index ce759d47370..78a9c1bfd20 100644 --- a/target/nextflow/metadata/join_csv/main.nf +++ b/target/nextflow/metadata/join_csv/main.nf @@ -1,4 +1,4 @@ -// join_csv 1.0.1 +// join_csv 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "join_csv", "namespace" : "metadata", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3099,9 +3099,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/join_csv", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/metadata/join_csv/nextflow.config b/target/nextflow/metadata/join_csv/nextflow.config index 816ca0f3a65..fce7ff8dd80 100644 --- a/target/nextflow/metadata/join_csv/nextflow.config +++ b/target/nextflow/metadata/join_csv/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'metadata/join_csv' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Join a csv containing metadata to the .obs or .var field of a mudata file.' author = 'Dries Schaumont' } diff --git a/target/nextflow/metadata/join_uns_to_obs/.config.vsh.yaml b/target/nextflow/metadata/join_uns_to_obs/.config.vsh.yaml index 04c518db804..fd4524c688f 100644 --- a/target/nextflow/metadata/join_uns_to_obs/.config.vsh.yaml +++ b/target/nextflow/metadata/join_uns_to_obs/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "join_uns_to_obs" namespace: "metadata" - version: "1.0.1" + version: "1.0.2" arguments: - type: "file" name: "--input" @@ -183,6 +183,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/join_uns_to_obs" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/join_uns_to_obs/join_uns_to_obs" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/metadata/join_uns_to_obs/main.nf b/target/nextflow/metadata/join_uns_to_obs/main.nf index 18cecf69355..6bce64ba014 100644 --- a/target/nextflow/metadata/join_uns_to_obs/main.nf +++ b/target/nextflow/metadata/join_uns_to_obs/main.nf @@ -1,4 +1,4 @@ -// join_uns_to_obs 1.0.1 +// join_uns_to_obs 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2782,7 +2782,7 @@ meta = [ "functionality" : { "name" : "join_uns_to_obs", "namespace" : "metadata", - "version" : "1.0.1", + "version" : "1.0.2", "arguments" : [ { "type" : "file", @@ -3018,9 +3018,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/join_uns_to_obs", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/metadata/join_uns_to_obs/nextflow.config b/target/nextflow/metadata/join_uns_to_obs/nextflow.config index fad52854f7d..9f67915e264 100644 --- a/target/nextflow/metadata/join_uns_to_obs/nextflow.config +++ b/target/nextflow/metadata/join_uns_to_obs/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'metadata/join_uns_to_obs' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Join a data frame of length 1 (1 row index value) in .uns containing metadata to the .obs of a mudata file.' } diff --git a/target/nextflow/metadata/move_obsm_to_obs/.config.vsh.yaml b/target/nextflow/metadata/move_obsm_to_obs/.config.vsh.yaml index ac283c7d316..92e050937ed 100644 --- a/target/nextflow/metadata/move_obsm_to_obs/.config.vsh.yaml +++ b/target/nextflow/metadata/move_obsm_to_obs/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "move_obsm_to_obs" namespace: "metadata" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -204,6 +204,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/move_obsm_to_obs" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/move_obsm_to_obs/move_obsm_to_obs" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/metadata/move_obsm_to_obs/main.nf b/target/nextflow/metadata/move_obsm_to_obs/main.nf index d2bbe0535f7..64218c23684 100644 --- a/target/nextflow/metadata/move_obsm_to_obs/main.nf +++ b/target/nextflow/metadata/move_obsm_to_obs/main.nf @@ -1,4 +1,4 @@ -// move_obsm_to_obs 1.0.1 +// move_obsm_to_obs 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "move_obsm_to_obs", "namespace" : "metadata", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3056,9 +3056,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/move_obsm_to_obs", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/metadata/move_obsm_to_obs/nextflow.config b/target/nextflow/metadata/move_obsm_to_obs/nextflow.config index 13322056ebe..7acdf6e121a 100644 --- a/target/nextflow/metadata/move_obsm_to_obs/nextflow.config +++ b/target/nextflow/metadata/move_obsm_to_obs/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'metadata/move_obsm_to_obs' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Move a matrix from .obsm to .obs. Newly created columns in .obs will \nbe created from the .obsm key suffixed with an underscore and the name of the columns\nof the specified .obsm matrix.\n' author = 'Dries Schaumont' } diff --git a/target/nextflow/neighbors/bbknn/.config.vsh.yaml b/target/nextflow/neighbors/bbknn/.config.vsh.yaml index 2b630be8c14..69e6c9ae86d 100644 --- a/target/nextflow/neighbors/bbknn/.config.vsh.yaml +++ b/target/nextflow/neighbors/bbknn/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "bbknn" namespace: "neighbors" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries De Maeyer" roles: @@ -294,6 +294,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/neighbors/bbknn" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/neighbors/bbknn/bbknn" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/neighbors/bbknn/main.nf b/target/nextflow/neighbors/bbknn/main.nf index 6c08c0990a8..84c43bcc147 100644 --- a/target/nextflow/neighbors/bbknn/main.nf +++ b/target/nextflow/neighbors/bbknn/main.nf @@ -1,4 +1,4 @@ -// bbknn 1.0.1 +// bbknn 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2786,7 +2786,7 @@ meta = [ "functionality" : { "name" : "bbknn", "namespace" : "neighbors", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries De Maeyer", @@ -3147,9 +3147,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/neighbors/bbknn", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/neighbors/bbknn/nextflow.config b/target/nextflow/neighbors/bbknn/nextflow.config index cf9178b2d88..7a625762b67 100644 --- a/target/nextflow/neighbors/bbknn/nextflow.config +++ b/target/nextflow/neighbors/bbknn/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'neighbors/bbknn' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'BBKNN network generation\n' author = 'Dries De Maeyer, Dries Schaumont' } diff --git a/target/nextflow/neighbors/find_neighbors/.config.vsh.yaml b/target/nextflow/neighbors/find_neighbors/.config.vsh.yaml index 37445bc89c5..da33466dc5c 100644 --- a/target/nextflow/neighbors/find_neighbors/.config.vsh.yaml +++ b/target/nextflow/neighbors/find_neighbors/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "find_neighbors" namespace: "neighbors" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries De Maeyer" roles: @@ -314,6 +314,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/neighbors/find_neighbors" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/neighbors/find_neighbors/find_neighbors" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/neighbors/find_neighbors/main.nf b/target/nextflow/neighbors/find_neighbors/main.nf index a8c0a962a4e..347c3550b12 100644 --- a/target/nextflow/neighbors/find_neighbors/main.nf +++ b/target/nextflow/neighbors/find_neighbors/main.nf @@ -1,4 +1,4 @@ -// find_neighbors 1.0.1 +// find_neighbors 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2786,7 +2786,7 @@ meta = [ "functionality" : { "name" : "find_neighbors", "namespace" : "neighbors", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries De Maeyer", @@ -3172,9 +3172,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/neighbors/find_neighbors", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/neighbors/find_neighbors/nextflow.config b/target/nextflow/neighbors/find_neighbors/nextflow.config index d8c0f71c975..6c091c26c6c 100644 --- a/target/nextflow/neighbors/find_neighbors/nextflow.config +++ b/target/nextflow/neighbors/find_neighbors/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'neighbors/find_neighbors' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Compute a neighborhood graph of observations [McInnes18].\n\nThe neighbor search efficiency of this heavily relies on UMAP [McInnes18], which also provides a method for estimating connectivities of data points - the connectivity of the manifold (method==\'umap\'). If method==\'gauss\', connectivities are computed according to [Coifman05], in the adaption of [Haghverdi16].\n' author = 'Dries De Maeyer, Robrecht Cannoodt' } diff --git a/target/nextflow/process_10xh5/filter_10xh5/.config.vsh.yaml b/target/nextflow/process_10xh5/filter_10xh5/.config.vsh.yaml index 14fe3dde2af..8bb9663cc93 100644 --- a/target/nextflow/process_10xh5/filter_10xh5/.config.vsh.yaml +++ b/target/nextflow/process_10xh5/filter_10xh5/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "filter_10xh5" namespace: "process_10xh5" - version: "1.0.1" + version: "1.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -200,6 +200,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/process_10xh5/filter_10xh5" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/process_10xh5/filter_10xh5/filter_10xh5" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/process_10xh5/filter_10xh5/main.nf b/target/nextflow/process_10xh5/filter_10xh5/main.nf index 1aa23cbe3a5..1b1800c278c 100644 --- a/target/nextflow/process_10xh5/filter_10xh5/main.nf +++ b/target/nextflow/process_10xh5/filter_10xh5/main.nf @@ -1,4 +1,4 @@ -// filter_10xh5 1.0.1 +// filter_10xh5 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "filter_10xh5", "namespace" : "process_10xh5", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -3040,9 +3040,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/process_10xh5/filter_10xh5", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/process_10xh5/filter_10xh5/nextflow.config b/target/nextflow/process_10xh5/filter_10xh5/nextflow.config index 0648ad927c5..254a5c72813 100644 --- a/target/nextflow/process_10xh5/filter_10xh5/nextflow.config +++ b/target/nextflow/process_10xh5/filter_10xh5/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'process_10xh5/filter_10xh5' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Filter a 10x h5 dataset.\n' author = 'Robrecht Cannoodt' } diff --git a/target/nextflow/qc/calculate_qc_metrics/.config.vsh.yaml b/target/nextflow/qc/calculate_qc_metrics/.config.vsh.yaml index 5231144e6b5..f5f399ff7ed 100644 --- a/target/nextflow/qc/calculate_qc_metrics/.config.vsh.yaml +++ b/target/nextflow/qc/calculate_qc_metrics/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "calculate_qc_metrics" namespace: "qc" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -320,6 +320,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/qc/calculate_qc_metrics" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/qc/calculate_qc_metrics/calculate_qc_metrics" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/qc/calculate_qc_metrics/main.nf b/target/nextflow/qc/calculate_qc_metrics/main.nf index 9af0d2017f5..a67db37f413 100644 --- a/target/nextflow/qc/calculate_qc_metrics/main.nf +++ b/target/nextflow/qc/calculate_qc_metrics/main.nf @@ -1,4 +1,4 @@ -// calculate_qc_metrics 1.0.1 +// calculate_qc_metrics 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "calculate_qc_metrics", "namespace" : "qc", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3167,9 +3167,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/qc/calculate_qc_metrics", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/qc/calculate_qc_metrics/nextflow.config b/target/nextflow/qc/calculate_qc_metrics/nextflow.config index b22b65e7a25..17755a722a4 100644 --- a/target/nextflow/qc/calculate_qc_metrics/nextflow.config +++ b/target/nextflow/qc/calculate_qc_metrics/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'qc/calculate_qc_metrics' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Add basic quality control metrics to an .h5mu file.\n\nThe metrics are comparable to what scanpy.pp.calculate_qc_metrics output,\nalthough they have slightly different names:\n\nVar metrics (name in this component -> name in scanpy):\n - pct_dropout -> pct_dropout_by_{expr_type}\n - num_nonzero_obs -> n_cells_by_{expr_type}\n - obs_mean -> mean_{expr_type}\n - total_counts -> total_{expr_type}\n\nObs metrics:\n - num_nonzero_vars -> n_genes_by_{expr_type}\n - pct_{var_qc_metrics} -> pct_{expr_type}_{qc_var}\n - total_counts_{var_qc_metrics} -> total_{expr_type}_{qc_var}\n - pct_of_counts_in_top_{top_n_vars}_vars -> pct_{expr_type}_in_top_{n}_{var_type}\n - total_counts -> total_{expr_type}\n \n' author = 'Dries Schaumont' } diff --git a/target/nextflow/qc/fastqc/.config.vsh.yaml b/target/nextflow/qc/fastqc/.config.vsh.yaml index 7eba9907016..878ed241860 100644 --- a/target/nextflow/qc/fastqc/.config.vsh.yaml +++ b/target/nextflow/qc/fastqc/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "fastqc" namespace: "qc" - version: "1.0.1" + version: "1.0.2" arguments: - type: "string" name: "--mode" @@ -159,6 +159,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/qc/fastqc" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/qc/fastqc/fastqc" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/qc/fastqc/main.nf b/target/nextflow/qc/fastqc/main.nf index 7c952ff5d78..41edb26c21c 100644 --- a/target/nextflow/qc/fastqc/main.nf +++ b/target/nextflow/qc/fastqc/main.nf @@ -1,4 +1,4 @@ -// fastqc 1.0.1 +// fastqc 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2782,7 +2782,7 @@ meta = [ "functionality" : { "name" : "fastqc", "namespace" : "qc", - "version" : "1.0.1", + "version" : "1.0.2", "arguments" : [ { "type" : "string", @@ -2979,9 +2979,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/qc/fastqc", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/qc/fastqc/nextflow.config b/target/nextflow/qc/fastqc/nextflow.config index effca17a25a..3dba7193bda 100644 --- a/target/nextflow/qc/fastqc/nextflow.config +++ b/target/nextflow/qc/fastqc/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'qc/fastqc' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Fastqc component, please see https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. This component can take one or more files (by means of shell globbing) or a complete directory.\n' } diff --git a/target/nextflow/qc/multiqc/.config.vsh.yaml b/target/nextflow/qc/multiqc/.config.vsh.yaml index 287de39048f..4462583afbd 100644 --- a/target/nextflow/qc/multiqc/.config.vsh.yaml +++ b/target/nextflow/qc/multiqc/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "multiqc" namespace: "qc" - version: "1.0.1" + version: "1.0.2" arguments: - type: "file" name: "--input" @@ -143,6 +143,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/qc/multiqc" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/qc/multiqc/multiqc" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/qc/multiqc/main.nf b/target/nextflow/qc/multiqc/main.nf index 6a16522d709..f55ec95067b 100644 --- a/target/nextflow/qc/multiqc/main.nf +++ b/target/nextflow/qc/multiqc/main.nf @@ -1,4 +1,4 @@ -// multiqc 1.0.1 +// multiqc 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2782,7 +2782,7 @@ meta = [ "functionality" : { "name" : "multiqc", "namespace" : "qc", - "version" : "1.0.1", + "version" : "1.0.2", "arguments" : [ { "type" : "file", @@ -2964,9 +2964,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/qc/multiqc", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/qc/multiqc/nextflow.config b/target/nextflow/qc/multiqc/nextflow.config index 9d1b223ef18..3da91b94cfb 100644 --- a/target/nextflow/qc/multiqc/nextflow.config +++ b/target/nextflow/qc/multiqc/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'qc/multiqc' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'MultiQC aggregates results from bioinformatics analyses across many samples into a single report.\nIt searches a given directory for analysis logs and compiles a HTML report. It\'s a general use tool, perfect for summarising the output from numerous bioinformatics tools.\n' } diff --git a/target/nextflow/query/cellxgene_census/.config.vsh.yaml b/target/nextflow/query/cellxgene_census/.config.vsh.yaml index 6c9c8c1ddab..ebecabd2018 100644 --- a/target/nextflow/query/cellxgene_census/.config.vsh.yaml +++ b/target/nextflow/query/cellxgene_census/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "cellxgene_census" namespace: "query" - version: "1.0.1" + version: "1.0.2" authors: - name: "Matthias Beyens" roles: @@ -519,6 +519,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/query/cellxgene_census" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/query/cellxgene_census/cellxgene_census" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/query/cellxgene_census/main.nf b/target/nextflow/query/cellxgene_census/main.nf index a43e4a9e09c..a64df1cde42 100644 --- a/target/nextflow/query/cellxgene_census/main.nf +++ b/target/nextflow/query/cellxgene_census/main.nf @@ -1,4 +1,4 @@ -// cellxgene_census 1.0.1 +// cellxgene_census 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2788,7 +2788,7 @@ meta = [ "functionality" : { "name" : "cellxgene_census", "namespace" : "query", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Matthias Beyens", @@ -3420,9 +3420,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/query/cellxgene_census", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/query/cellxgene_census/nextflow.config b/target/nextflow/query/cellxgene_census/nextflow.config index 13014681911..a08632cdbde 100644 --- a/target/nextflow/query/cellxgene_census/nextflow.config +++ b/target/nextflow/query/cellxgene_census/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'query/cellxgene_census' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Query cells from a CellxGene Census or custom TileDBSoma object.\nAside from fetching the cells\' RNA counts (`.X`), cell metadata\n(`.obs`) and gene metadata (`.var`), this component also fetches\nthe dataset metadata and joins it into the cell metadata.\n' author = 'Matthias Beyens, Dries De Maeyer, Robrecht Cannoodt, Kai Waldrant' } diff --git a/target/nextflow/reference/build_bdrhap_reference/.config.vsh.yaml b/target/nextflow/reference/build_bdrhap_reference/.config.vsh.yaml index 9c5f999f838..9c1dbfe68a7 100644 --- a/target/nextflow/reference/build_bdrhap_reference/.config.vsh.yaml +++ b/target/nextflow/reference/build_bdrhap_reference/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "build_bdrhap_reference" namespace: "reference" - version: "1.0.1" + version: "1.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -188,6 +188,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/reference/build_bdrhap_reference" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/reference/build_bdrhap_reference/build_bdrhap_reference" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/reference/build_bdrhap_reference/main.nf b/target/nextflow/reference/build_bdrhap_reference/main.nf index 22f8de9485f..51b2d6b159d 100644 --- a/target/nextflow/reference/build_bdrhap_reference/main.nf +++ b/target/nextflow/reference/build_bdrhap_reference/main.nf @@ -1,4 +1,4 @@ -// build_bdrhap_reference 1.0.1 +// build_bdrhap_reference 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2786,7 +2786,7 @@ meta = [ "functionality" : { "name" : "build_bdrhap_reference", "namespace" : "reference", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Angela Oliveira Pisco", @@ -3031,9 +3031,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/reference/build_bdrhap_reference", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/reference/build_bdrhap_reference/nextflow.config b/target/nextflow/reference/build_bdrhap_reference/nextflow.config index dcf88ec3bac..3e3a7ea03bd 100644 --- a/target/nextflow/reference/build_bdrhap_reference/nextflow.config +++ b/target/nextflow/reference/build_bdrhap_reference/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'reference/build_bdrhap_reference' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Compile a reference into a STAR index compatible with the BD Rhapsody pipeline.' author = 'Angela Oliveira Pisco, Robrecht Cannoodt' } diff --git a/target/nextflow/reference/build_cellranger_reference/.config.vsh.yaml b/target/nextflow/reference/build_cellranger_reference/.config.vsh.yaml index 05b0c57fd20..18a298e2f07 100644 --- a/target/nextflow/reference/build_cellranger_reference/.config.vsh.yaml +++ b/target/nextflow/reference/build_cellranger_reference/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "build_cellranger_reference" namespace: "reference" - version: "1.0.1" + version: "1.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -188,6 +188,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/reference/build_cellranger_reference" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/reference/build_cellranger_reference/build_cellranger_reference" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/reference/build_cellranger_reference/main.nf b/target/nextflow/reference/build_cellranger_reference/main.nf index d34a28428bd..fe2665d8188 100644 --- a/target/nextflow/reference/build_cellranger_reference/main.nf +++ b/target/nextflow/reference/build_cellranger_reference/main.nf @@ -1,4 +1,4 @@ -// build_cellranger_reference 1.0.1 +// build_cellranger_reference 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2786,7 +2786,7 @@ meta = [ "functionality" : { "name" : "build_cellranger_reference", "namespace" : "reference", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Angela Oliveira Pisco", @@ -3030,9 +3030,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/reference/build_cellranger_reference", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/reference/build_cellranger_reference/nextflow.config b/target/nextflow/reference/build_cellranger_reference/nextflow.config index 4c16ba9d2e6..341794093f1 100644 --- a/target/nextflow/reference/build_cellranger_reference/nextflow.config +++ b/target/nextflow/reference/build_cellranger_reference/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'reference/build_cellranger_reference' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Build a Cell Ranger-compatible reference folder from user-supplied genome FASTA and gene GTF files. Creates a new folder named after the genome.' author = 'Angela Oliveira Pisco, Robrecht Cannoodt' } diff --git a/target/nextflow/reference/make_reference/.config.vsh.yaml b/target/nextflow/reference/make_reference/.config.vsh.yaml index 8cc218bd0a4..6d8e1256770 100644 --- a/target/nextflow/reference/make_reference/.config.vsh.yaml +++ b/target/nextflow/reference/make_reference/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "make_reference" namespace: "reference" - version: "1.0.1" + version: "1.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -215,6 +215,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/reference/make_reference" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/reference/make_reference/make_reference" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/reference/make_reference/main.nf b/target/nextflow/reference/make_reference/main.nf index 88b0a3448b7..4a776764612 100644 --- a/target/nextflow/reference/make_reference/main.nf +++ b/target/nextflow/reference/make_reference/main.nf @@ -1,4 +1,4 @@ -// make_reference 1.0.1 +// make_reference 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2786,7 +2786,7 @@ meta = [ "functionality" : { "name" : "make_reference", "namespace" : "reference", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Angela Oliveira Pisco", @@ -3057,9 +3057,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/reference/make_reference", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/reference/make_reference/nextflow.config b/target/nextflow/reference/make_reference/nextflow.config index 4b9a5dde7a5..a31442f6115 100644 --- a/target/nextflow/reference/make_reference/nextflow.config +++ b/target/nextflow/reference/make_reference/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'reference/make_reference' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Preprocess and build a transcriptome reference.\n\nExample input files are:\n - `genome_fasta`: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_41/GRCh38.primary_assembly.genome.fa.gz\n - `transcriptome_gtf`: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_41/gencode.v41.annotation.gtf.gz\n - `ercc`: https://assets.thermofisher.com/TFS-Assets/LSG/manuals/ERCC92.zip\n' author = 'Angela Oliveira Pisco, Robrecht Cannoodt' } diff --git a/target/nextflow/report/mermaid/.config.vsh.yaml b/target/nextflow/report/mermaid/.config.vsh.yaml index 1fa16a3e554..8ae4cf64ba4 100644 --- a/target/nextflow/report/mermaid/.config.vsh.yaml +++ b/target/nextflow/report/mermaid/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "mermaid" namespace: "report" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries De Maeyer" roles: @@ -188,6 +188,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/report/mermaid" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/report/mermaid/mermaid" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/report/mermaid/main.nf b/target/nextflow/report/mermaid/main.nf index 67db9cf824a..bda83a6499e 100644 --- a/target/nextflow/report/mermaid/main.nf +++ b/target/nextflow/report/mermaid/main.nf @@ -1,4 +1,4 @@ -// mermaid 1.0.1 +// mermaid 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "mermaid", "namespace" : "report", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries De Maeyer", @@ -3025,9 +3025,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/report/mermaid", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/report/mermaid/nextflow.config b/target/nextflow/report/mermaid/nextflow.config index c7ef4f4e95f..1ada81648ec 100644 --- a/target/nextflow/report/mermaid/nextflow.config +++ b/target/nextflow/report/mermaid/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'report/mermaid' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Generates a network from mermaid code.\n' author = 'Dries De Maeyer' } diff --git a/target/nextflow/transfer/publish/.config.vsh.yaml b/target/nextflow/transfer/publish/.config.vsh.yaml index f500addb1ae..9cda3d2e85c 100644 --- a/target/nextflow/transfer/publish/.config.vsh.yaml +++ b/target/nextflow/transfer/publish/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "publish" namespace: "transfer" - version: "1.0.1" + version: "1.0.2" authors: - name: "Toni Verbeiren" roles: @@ -128,6 +128,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/transfer/publish" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/transfer/publish/publish" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/transfer/publish/main.nf b/target/nextflow/transfer/publish/main.nf index 5ac910ca7e3..7d01cc9e147 100644 --- a/target/nextflow/transfer/publish/main.nf +++ b/target/nextflow/transfer/publish/main.nf @@ -1,4 +1,4 @@ -// publish 1.0.1 +// publish 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "publish", "namespace" : "transfer", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Toni Verbeiren", @@ -2947,9 +2947,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/transfer/publish", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/transfer/publish/nextflow.config b/target/nextflow/transfer/publish/nextflow.config index 2c799d95a5f..e4158c82369 100644 --- a/target/nextflow/transfer/publish/nextflow.config +++ b/target/nextflow/transfer/publish/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'transfer/publish' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Publish an artifact and optionally rename with parameters' author = 'Toni Verbeiren' } diff --git a/target/nextflow/transform/clr/.config.vsh.yaml b/target/nextflow/transform/clr/.config.vsh.yaml index 9ce69653467..2824f6031f6 100644 --- a/target/nextflow/transform/clr/.config.vsh.yaml +++ b/target/nextflow/transform/clr/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "clr" namespace: "transform" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -202,6 +202,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/clr" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/clr/clr" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/transform/clr/main.nf b/target/nextflow/transform/clr/main.nf index ed2f668049f..e4179916186 100644 --- a/target/nextflow/transform/clr/main.nf +++ b/target/nextflow/transform/clr/main.nf @@ -1,4 +1,4 @@ -// clr 1.0.1 +// clr 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "clr", "namespace" : "transform", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3045,9 +3045,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/clr", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/transform/clr/nextflow.config b/target/nextflow/transform/clr/nextflow.config index c6d989d4ef2..6808a77c155 100644 --- a/target/nextflow/transform/clr/nextflow.config +++ b/target/nextflow/transform/clr/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'transform/clr' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Perform CLR normalization on CITE-seq data (Stoeckius et al., 2017).\n' author = 'Dries Schaumont' } diff --git a/target/nextflow/transform/delete_layer/.config.vsh.yaml b/target/nextflow/transform/delete_layer/.config.vsh.yaml index e18287cebfd..3e767d0e74c 100644 --- a/target/nextflow/transform/delete_layer/.config.vsh.yaml +++ b/target/nextflow/transform/delete_layer/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "delete_layer" namespace: "transform" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -200,6 +200,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/delete_layer" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/delete_layer/delete_layer" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/transform/delete_layer/main.nf b/target/nextflow/transform/delete_layer/main.nf index 832e72d7f42..1068bf0ffa8 100644 --- a/target/nextflow/transform/delete_layer/main.nf +++ b/target/nextflow/transform/delete_layer/main.nf @@ -1,4 +1,4 @@ -// delete_layer 1.0.1 +// delete_layer 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "delete_layer", "namespace" : "transform", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3049,9 +3049,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/delete_layer", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/transform/delete_layer/nextflow.config b/target/nextflow/transform/delete_layer/nextflow.config index de1750c812a..58cdaf8e725 100644 --- a/target/nextflow/transform/delete_layer/nextflow.config +++ b/target/nextflow/transform/delete_layer/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'transform/delete_layer' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Delete an anndata layer from one or more modalities.\n' author = 'Dries Schaumont' } diff --git a/target/nextflow/transform/log1p/.config.vsh.yaml b/target/nextflow/transform/log1p/.config.vsh.yaml index 9fc5962dff7..9e2c0fffacf 100644 --- a/target/nextflow/transform/log1p/.config.vsh.yaml +++ b/target/nextflow/transform/log1p/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "log1p" namespace: "transform" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries De Maeyer" roles: @@ -230,6 +230,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/log1p" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/log1p/log1p" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/transform/log1p/main.nf b/target/nextflow/transform/log1p/main.nf index 2362fb3ab4d..79f20260d92 100644 --- a/target/nextflow/transform/log1p/main.nf +++ b/target/nextflow/transform/log1p/main.nf @@ -1,4 +1,4 @@ -// log1p 1.0.1 +// log1p 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2786,7 +2786,7 @@ meta = [ "functionality" : { "name" : "log1p", "namespace" : "transform", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries De Maeyer", @@ -3088,9 +3088,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/log1p", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/transform/log1p/nextflow.config b/target/nextflow/transform/log1p/nextflow.config index 18739eeec1f..463c5e725bf 100644 --- a/target/nextflow/transform/log1p/nextflow.config +++ b/target/nextflow/transform/log1p/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'transform/log1p' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Logarithmize the data matrix. Computes X = log(X + 1), where log denotes the natural logarithm unless a different base is given.\n' author = 'Dries De Maeyer, Robrecht Cannoodt' } diff --git a/target/nextflow/transform/move_layer/.config.vsh.yaml b/target/nextflow/transform/move_layer/.config.vsh.yaml index 2f67c5eea06..0b55904fd34 100644 --- a/target/nextflow/transform/move_layer/.config.vsh.yaml +++ b/target/nextflow/transform/move_layer/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "move_layer" namespace: "transform" - version: "1.0.1" + version: "1.0.2" arguments: - type: "file" name: "--input" @@ -183,6 +183,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/move_layer" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/move_layer/move_layer" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/transform/move_layer/main.nf b/target/nextflow/transform/move_layer/main.nf index 29215ddb202..f10175ae1ae 100644 --- a/target/nextflow/transform/move_layer/main.nf +++ b/target/nextflow/transform/move_layer/main.nf @@ -1,4 +1,4 @@ -// move_layer 1.0.1 +// move_layer 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2782,7 +2782,7 @@ meta = [ "functionality" : { "name" : "move_layer", "namespace" : "transform", - "version" : "1.0.1", + "version" : "1.0.2", "arguments" : [ { "type" : "file", @@ -3013,9 +3013,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/move_layer", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/transform/move_layer/nextflow.config b/target/nextflow/transform/move_layer/nextflow.config index ce29a4cca37..916211cf779 100644 --- a/target/nextflow/transform/move_layer/nextflow.config +++ b/target/nextflow/transform/move_layer/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'transform/move_layer' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Move a data matrix stored at the .layers or .X attributes in a MuData object to another layer.' } diff --git a/target/nextflow/transform/normalize_total/.config.vsh.yaml b/target/nextflow/transform/normalize_total/.config.vsh.yaml index 028224ffe90..6eb10308d4b 100644 --- a/target/nextflow/transform/normalize_total/.config.vsh.yaml +++ b/target/nextflow/transform/normalize_total/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "normalize_total" namespace: "transform" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries De Maeyer" roles: @@ -247,6 +247,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/normalize_total" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/normalize_total/normalize_total" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/transform/normalize_total/main.nf b/target/nextflow/transform/normalize_total/main.nf index b3815d34119..d5bd81d54ed 100644 --- a/target/nextflow/transform/normalize_total/main.nf +++ b/target/nextflow/transform/normalize_total/main.nf @@ -1,4 +1,4 @@ -// normalize_total 1.0.1 +// normalize_total 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2786,7 +2786,7 @@ meta = [ "functionality" : { "name" : "normalize_total", "namespace" : "transform", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries De Maeyer", @@ -3097,9 +3097,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/normalize_total", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/transform/normalize_total/nextflow.config b/target/nextflow/transform/normalize_total/nextflow.config index 859bc116ec5..190e5045dc2 100644 --- a/target/nextflow/transform/normalize_total/nextflow.config +++ b/target/nextflow/transform/normalize_total/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'transform/normalize_total' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Normalize counts per cell.\n\nNormalize each cell by total counts over all genes, so that every cell has the same total count after normalization. If choosing target_sum=1e6, this is CPM normalization.\n\nIf exclude_highly_expressed=True, very highly expressed genes are excluded from the computation of the normalization factor (size factor) for each cell. This is meaningful as these can strongly influence the resulting normalized values for all other genes [Weinreb17].\n' author = 'Dries De Maeyer, Robrecht Cannoodt' } diff --git a/target/nextflow/transform/regress_out/.config.vsh.yaml b/target/nextflow/transform/regress_out/.config.vsh.yaml index dc910b42a09..deaf209219e 100644 --- a/target/nextflow/transform/regress_out/.config.vsh.yaml +++ b/target/nextflow/transform/regress_out/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "regress_out" namespace: "transform" - version: "1.0.1" + version: "1.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -200,6 +200,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/regress_out" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/regress_out/regress_out" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/transform/regress_out/main.nf b/target/nextflow/transform/regress_out/main.nf index a23713a6388..62c313a006b 100644 --- a/target/nextflow/transform/regress_out/main.nf +++ b/target/nextflow/transform/regress_out/main.nf @@ -1,4 +1,4 @@ -// regress_out 1.0.1 +// regress_out 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "regress_out", "namespace" : "transform", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -3043,9 +3043,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/regress_out", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/transform/regress_out/nextflow.config b/target/nextflow/transform/regress_out/nextflow.config index d07711a0a65..558e78b69de 100644 --- a/target/nextflow/transform/regress_out/nextflow.config +++ b/target/nextflow/transform/regress_out/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'transform/regress_out' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Regress out (mostly) unwanted sources of variation.\nUses simple linear regression. This is inspired by Seurat\'s regressOut function in R [Satija15]. \nNote that this function tends to overcorrect in certain circumstances as described in issue theislab/scanpy#526.\nSee https://github.com/theislab/scanpy/issues/526.\n' author = 'Robrecht Cannoodt' } diff --git a/target/nextflow/transform/scale/.config.vsh.yaml b/target/nextflow/transform/scale/.config.vsh.yaml index 790ca1fc497..4fcf176071c 100644 --- a/target/nextflow/transform/scale/.config.vsh.yaml +++ b/target/nextflow/transform/scale/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "scale" namespace: "transform" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -210,6 +210,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/scale" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/scale/scale" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/transform/scale/main.nf b/target/nextflow/transform/scale/main.nf index 29b62d4a05f..ffa4be239f7 100644 --- a/target/nextflow/transform/scale/main.nf +++ b/target/nextflow/transform/scale/main.nf @@ -1,4 +1,4 @@ -// scale 1.0.1 +// scale 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "scale", "namespace" : "transform", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3058,9 +3058,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/scale", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/transform/scale/nextflow.config b/target/nextflow/transform/scale/nextflow.config index 9e19fc26abb..c096e8f208c 100644 --- a/target/nextflow/transform/scale/nextflow.config +++ b/target/nextflow/transform/scale/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'transform/scale' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Scale data to unit variance and zero mean.\n' author = 'Dries Schaumont' } diff --git a/target/nextflow/velocity/scvelo/.config.vsh.yaml b/target/nextflow/velocity/scvelo/.config.vsh.yaml index f0ce2fefac2..5155dca56aa 100644 --- a/target/nextflow/velocity/scvelo/.config.vsh.yaml +++ b/target/nextflow/velocity/scvelo/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "scvelo" namespace: "velocity" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -282,6 +282,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/velocity/scvelo" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/velocity/scvelo/scvelo" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/velocity/scvelo/main.nf b/target/nextflow/velocity/scvelo/main.nf index 35f643ebb4a..bb60eb2a588 100644 --- a/target/nextflow/velocity/scvelo/main.nf +++ b/target/nextflow/velocity/scvelo/main.nf @@ -1,4 +1,4 @@ -// scvelo 1.0.1 +// scvelo 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "scvelo", "namespace" : "velocity", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3139,9 +3139,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/velocity/scvelo", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/velocity/scvelo/nextflow.config b/target/nextflow/velocity/scvelo/nextflow.config index 155203353a6..d932966f48f 100644 --- a/target/nextflow/velocity/scvelo/nextflow.config +++ b/target/nextflow/velocity/scvelo/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'velocity/scvelo' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' author = 'Dries Schaumont' } diff --git a/target/nextflow/velocity/velocyto/.config.vsh.yaml b/target/nextflow/velocity/velocyto/.config.vsh.yaml index 7ffbcdf1422..afdc7fb72db 100644 --- a/target/nextflow/velocity/velocyto/.config.vsh.yaml +++ b/target/nextflow/velocity/velocyto/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "velocyto" namespace: "velocity" - version: "1.0.1" + version: "1.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -228,6 +228,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/velocity/velocyto" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/velocity/velocyto/velocyto" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/velocity/velocyto/main.nf b/target/nextflow/velocity/velocyto/main.nf index 4b4481c0243..94b345d09f4 100644 --- a/target/nextflow/velocity/velocyto/main.nf +++ b/target/nextflow/velocity/velocyto/main.nf @@ -1,4 +1,4 @@ -// velocyto 1.0.1 +// velocyto 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "velocyto", "namespace" : "velocity", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -3085,9 +3085,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/velocity/velocyto", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/velocity/velocyto/nextflow.config b/target/nextflow/velocity/velocyto/nextflow.config index def1840c019..f227279d0f8 100644 --- a/target/nextflow/velocity/velocyto/nextflow.config +++ b/target/nextflow/velocity/velocyto/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'velocity/velocyto' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Runs the velocity analysis on a BAM file, outputting a loom file.' author = 'Robrecht Cannoodt' } diff --git a/target/nextflow/workflows/gdo/gdo_singlesample/.config.vsh.yaml b/target/nextflow/workflows/gdo/gdo_singlesample/.config.vsh.yaml index 6d328beec97..5e1388974b9 100644 --- a/target/nextflow/workflows/gdo/gdo_singlesample/.config.vsh.yaml +++ b/target/nextflow/workflows/gdo/gdo_singlesample/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "gdo_singlesample" namespace: "workflows/gdo" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -160,14 +160,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/filter/filter_with_counts/config.vsh.yaml" configInfo: functionalityName: "filter_with_counts" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/filter/filter_with_counts/config.vsh.yaml" functionalityNamespace: "filter" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/filter/filter_with_counts/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/filter_with_counts" - name: "filter/do_filter" @@ -177,14 +177,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/filter/do_filter/config.vsh.yaml" configInfo: functionalityName: "do_filter" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/filter/do_filter/config.vsh.yaml" functionalityNamespace: "filter" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/filter/do_filter/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/do_filter" set_wd_to_resources_dir: false @@ -240,6 +240,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/gdo/gdo_singlesample" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/gdo/gdo_singlesample/main.nf" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/workflows/gdo/gdo_singlesample/main.nf b/target/nextflow/workflows/gdo/gdo_singlesample/main.nf index bc6e975e103..ff14acf1b4d 100644 --- a/target/nextflow/workflows/gdo/gdo_singlesample/main.nf +++ b/target/nextflow/workflows/gdo/gdo_singlesample/main.nf @@ -1,4 +1,4 @@ -// gdo_singlesample 1.0.1 +// gdo_singlesample 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "gdo_singlesample", "namespace" : "workflows/gdo", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3000,14 +3000,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/filter/filter_with_counts/config.vsh.yaml", "configInfo" : { "functionalityName" : "filter_with_counts", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/filter/filter_with_counts/config.vsh.yaml", "functionalityNamespace" : "filter", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/filter/filter_with_counts/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/filter_with_counts" @@ -3021,14 +3021,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/filter/do_filter/config.vsh.yaml", "configInfo" : { "functionalityName" : "do_filter", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/filter/do_filter/config.vsh.yaml", "functionalityNamespace" : "filter", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/filter/do_filter/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/do_filter" @@ -3095,9 +3095,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/gdo/gdo_singlesample", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/workflows/gdo/gdo_singlesample/nextflow.config b/target/nextflow/workflows/gdo/gdo_singlesample/nextflow.config index d597411e564..e33fafd14d2 100644 --- a/target/nextflow/workflows/gdo/gdo_singlesample/nextflow.config +++ b/target/nextflow/workflows/gdo/gdo_singlesample/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/gdo/gdo_singlesample' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Processing unimodal single-sample guide-derived oligonucleotide (GDO) data.' author = 'Dries Schaumont' } diff --git a/target/nextflow/workflows/ingestion/bd_rhapsody/.config.vsh.yaml b/target/nextflow/workflows/ingestion/bd_rhapsody/.config.vsh.yaml index bd34a0104f7..507de29ff84 100644 --- a/target/nextflow/workflows/ingestion/bd_rhapsody/.config.vsh.yaml +++ b/target/nextflow/workflows/ingestion/bd_rhapsody/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "bd_rhapsody" namespace: "workflows/ingestion" - version: "1.0.1" + version: "1.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -366,14 +366,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/mapping/bd_rhapsody/config.vsh.yaml" configInfo: functionalityName: "bd_rhapsody" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/mapping/bd_rhapsody/config.vsh.yaml" functionalityNamespace: "mapping" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/mapping/bd_rhapsody/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/bd_rhapsody" - name: "convert/from_bdrhap_to_h5mu" @@ -383,14 +383,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/convert/from_bdrhap_to_h5mu/config.vsh.yaml" configInfo: functionalityName: "from_bdrhap_to_h5mu" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/convert/from_bdrhap_to_h5mu/config.vsh.yaml" functionalityNamespace: "convert" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/convert/from_bdrhap_to_h5mu/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_bdrhap_to_h5mu" set_wd_to_resources_dir: false @@ -446,6 +446,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/ingestion/bd_rhapsody" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/ingestion/bd_rhapsody/main.nf" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/workflows/ingestion/bd_rhapsody/main.nf b/target/nextflow/workflows/ingestion/bd_rhapsody/main.nf index ab8360de5dd..df50d170fdd 100644 --- a/target/nextflow/workflows/ingestion/bd_rhapsody/main.nf +++ b/target/nextflow/workflows/ingestion/bd_rhapsody/main.nf @@ -1,4 +1,4 @@ -// bd_rhapsody 1.0.1 +// bd_rhapsody 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "bd_rhapsody", "namespace" : "workflows/ingestion", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -3226,14 +3226,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/mapping/bd_rhapsody/config.vsh.yaml", "configInfo" : { "functionalityName" : "bd_rhapsody", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/mapping/bd_rhapsody/config.vsh.yaml", "functionalityNamespace" : "mapping", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/mapping/bd_rhapsody/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/bd_rhapsody" @@ -3247,14 +3247,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/convert/from_bdrhap_to_h5mu/config.vsh.yaml", "configInfo" : { "functionalityName" : "from_bdrhap_to_h5mu", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/convert/from_bdrhap_to_h5mu/config.vsh.yaml", "functionalityNamespace" : "convert", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/convert/from_bdrhap_to_h5mu/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_bdrhap_to_h5mu" @@ -3321,9 +3321,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/ingestion/bd_rhapsody", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/workflows/ingestion/bd_rhapsody/nextflow.config b/target/nextflow/workflows/ingestion/bd_rhapsody/nextflow.config index a5ce63814ec..73c0e606eb7 100644 --- a/target/nextflow/workflows/ingestion/bd_rhapsody/nextflow.config +++ b/target/nextflow/workflows/ingestion/bd_rhapsody/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/ingestion/bd_rhapsody' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'A wrapper for the BD Rhapsody Analysis CWL v1.10.1 pipeline.\n\nThis pipeline can be used for a targeted analysis (with `--mode targeted`) or for a whole transcriptome analysis (with `--mode wta`).\n\n* If mode is `"targeted"`, then either the `--reference` or `--abseq_reference` parameters must be defined.\n* If mode is `"wta"`, then `--reference` and `--transcriptome_annotation` must be defined, `--abseq_reference` and `--supplemental_reference` is optional.\n\nThe reference_genome and transcriptome_annotation files can be generated with the make_reference pipeline.\nAlternatively, BD also provides standard references which can be downloaded from these locations:\n\n - Human: http://bd-rhapsody-public.s3-website-us-east-1.amazonaws.com/Rhapsody-WTA/GRCh38-PhiX-gencodev29/\n - Mouse: http://bd-rhapsody-public.s3-website-us-east-1.amazonaws.com/Rhapsody-WTA/GRCm38-PhiX-gencodevM19/\n' author = 'Robrecht Cannoodt' } diff --git a/target/nextflow/workflows/ingestion/cellranger_mapping/.config.vsh.yaml b/target/nextflow/workflows/ingestion/cellranger_mapping/.config.vsh.yaml index 3ff1e2cb46c..e39fef82f8a 100644 --- a/target/nextflow/workflows/ingestion/cellranger_mapping/.config.vsh.yaml +++ b/target/nextflow/workflows/ingestion/cellranger_mapping/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "cellranger_mapping" namespace: "workflows/ingestion" - version: "1.0.1" + version: "1.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -257,14 +257,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/mapping/cellranger_count/config.vsh.yaml" configInfo: functionalityName: "cellranger_count" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/mapping/cellranger_count/config.vsh.yaml" functionalityNamespace: "mapping" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/mapping/cellranger_count/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/cellranger_count" - name: "mapping/cellranger_count_split" @@ -274,14 +274,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/mapping/cellranger_count_split/config.vsh.yaml" configInfo: functionalityName: "cellranger_count_split" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/mapping/cellranger_count_split/config.vsh.yaml" functionalityNamespace: "mapping" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/mapping/cellranger_count_split/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/cellranger_count_split" - name: "convert/from_10xh5_to_h5mu" @@ -291,14 +291,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/convert/from_10xh5_to_h5mu/config.vsh.yaml" configInfo: functionalityName: "from_10xh5_to_h5mu" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/convert/from_10xh5_to_h5mu/config.vsh.yaml" functionalityNamespace: "convert" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/convert/from_10xh5_to_h5mu/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_10xh5_to_h5mu" set_wd_to_resources_dir: false @@ -354,6 +354,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/ingestion/cellranger_mapping" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/ingestion/cellranger_mapping/main.nf" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/workflows/ingestion/cellranger_mapping/main.nf b/target/nextflow/workflows/ingestion/cellranger_mapping/main.nf index 947823f0bd9..12b3026c332 100644 --- a/target/nextflow/workflows/ingestion/cellranger_mapping/main.nf +++ b/target/nextflow/workflows/ingestion/cellranger_mapping/main.nf @@ -1,4 +1,4 @@ -// cellranger_mapping 1.0.1 +// cellranger_mapping 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2787,7 +2787,7 @@ meta = [ "functionality" : { "name" : "cellranger_mapping", "namespace" : "workflows/ingestion", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Angela Oliveira Pisco", @@ -3122,14 +3122,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/mapping/cellranger_count/config.vsh.yaml", "configInfo" : { "functionalityName" : "cellranger_count", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/mapping/cellranger_count/config.vsh.yaml", "functionalityNamespace" : "mapping", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/mapping/cellranger_count/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/cellranger_count" @@ -3143,14 +3143,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/mapping/cellranger_count_split/config.vsh.yaml", "configInfo" : { "functionalityName" : "cellranger_count_split", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/mapping/cellranger_count_split/config.vsh.yaml", "functionalityNamespace" : "mapping", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/mapping/cellranger_count_split/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/cellranger_count_split" @@ -3164,14 +3164,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/convert/from_10xh5_to_h5mu/config.vsh.yaml", "configInfo" : { "functionalityName" : "from_10xh5_to_h5mu", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/convert/from_10xh5_to_h5mu/config.vsh.yaml", "functionalityNamespace" : "convert", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/convert/from_10xh5_to_h5mu/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_10xh5_to_h5mu" @@ -3238,9 +3238,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/ingestion/cellranger_mapping", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/workflows/ingestion/cellranger_mapping/nextflow.config b/target/nextflow/workflows/ingestion/cellranger_mapping/nextflow.config index 9ad74207fc0..80cf28df9c6 100644 --- a/target/nextflow/workflows/ingestion/cellranger_mapping/nextflow.config +++ b/target/nextflow/workflows/ingestion/cellranger_mapping/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/ingestion/cellranger_mapping' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'A pipeline for running Cell Ranger mapping.' author = 'Angela Oliveira Pisco, Robrecht Cannoodt, Dries De Maeyer' } diff --git a/target/nextflow/workflows/ingestion/cellranger_multi/.config.vsh.yaml b/target/nextflow/workflows/ingestion/cellranger_multi/.config.vsh.yaml index 17c74846589..79235a9d21c 100644 --- a/target/nextflow/workflows/ingestion/cellranger_multi/.config.vsh.yaml +++ b/target/nextflow/workflows/ingestion/cellranger_multi/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "cellranger_multi" namespace: "workflows/ingestion" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -493,14 +493,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/mapping/cellranger_multi/config.vsh.yaml" configInfo: functionalityName: "cellranger_multi" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/mapping/cellranger_multi/config.vsh.yaml" functionalityNamespace: "mapping" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/mapping/cellranger_multi/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/cellranger_multi" - name: "convert/from_cellranger_multi_to_h5mu" @@ -510,14 +510,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/convert/from_cellranger_multi_to_h5mu/config.vsh.yaml" configInfo: functionalityName: "from_cellranger_multi_to_h5mu" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/convert/from_cellranger_multi_to_h5mu/config.vsh.yaml" functionalityNamespace: "convert" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/convert/from_cellranger_multi_to_h5mu/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_cellranger_multi_to_h5mu" set_wd_to_resources_dir: false @@ -573,6 +573,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/ingestion/cellranger_multi" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/ingestion/cellranger_multi/main.nf" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/workflows/ingestion/cellranger_multi/main.nf b/target/nextflow/workflows/ingestion/cellranger_multi/main.nf index 402b202a9f1..ecbb7ee15c6 100644 --- a/target/nextflow/workflows/ingestion/cellranger_multi/main.nf +++ b/target/nextflow/workflows/ingestion/cellranger_multi/main.nf @@ -1,4 +1,4 @@ -// cellranger_multi 1.0.1 +// cellranger_multi 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "cellranger_multi", "namespace" : "workflows/ingestion", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3346,14 +3346,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/mapping/cellranger_multi/config.vsh.yaml", "configInfo" : { "functionalityName" : "cellranger_multi", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/mapping/cellranger_multi/config.vsh.yaml", "functionalityNamespace" : "mapping", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/mapping/cellranger_multi/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/cellranger_multi" @@ -3367,14 +3367,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/convert/from_cellranger_multi_to_h5mu/config.vsh.yaml", "configInfo" : { "functionalityName" : "from_cellranger_multi_to_h5mu", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/convert/from_cellranger_multi_to_h5mu/config.vsh.yaml", "functionalityNamespace" : "convert", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/convert/from_cellranger_multi_to_h5mu/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_cellranger_multi_to_h5mu" @@ -3441,9 +3441,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/ingestion/cellranger_multi", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/workflows/ingestion/cellranger_multi/nextflow.config b/target/nextflow/workflows/ingestion/cellranger_multi/nextflow.config index b6645ed4aa8..8365378ace0 100644 --- a/target/nextflow/workflows/ingestion/cellranger_multi/nextflow.config +++ b/target/nextflow/workflows/ingestion/cellranger_multi/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/ingestion/cellranger_multi' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'A pipeline for running Cell Ranger multi.' author = 'Dries Schaumont' } diff --git a/target/nextflow/workflows/ingestion/cellranger_postprocessing/.config.vsh.yaml b/target/nextflow/workflows/ingestion/cellranger_postprocessing/.config.vsh.yaml index 013deba7a6f..46636c2f95a 100644 --- a/target/nextflow/workflows/ingestion/cellranger_postprocessing/.config.vsh.yaml +++ b/target/nextflow/workflows/ingestion/cellranger_postprocessing/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "cellranger_postprocessing" namespace: "workflows/ingestion" - version: "1.0.1" + version: "1.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -161,14 +161,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/correction/cellbender_remove_background/config.vsh.yaml" configInfo: functionalityName: "cellbender_remove_background" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/correction/cellbender_remove_background/config.vsh.yaml" functionalityNamespace: "correction" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/correction/cellbender_remove_background/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/correction/cellbender_remove_background" - name: "filter/filter_with_counts" @@ -178,14 +178,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/filter/filter_with_counts/config.vsh.yaml" configInfo: functionalityName: "filter_with_counts" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/filter/filter_with_counts/config.vsh.yaml" functionalityNamespace: "filter" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/filter/filter_with_counts/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/filter_with_counts" - name: "filter/subset_h5mu" @@ -195,14 +195,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/filter/subset_h5mu/config.vsh.yaml" configInfo: functionalityName: "subset_h5mu" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/filter/subset_h5mu/config.vsh.yaml" functionalityNamespace: "filter" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/filter/subset_h5mu/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/subset_h5mu" - name: "transfer/publish" @@ -212,14 +212,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/transfer/publish/config.vsh.yaml" configInfo: functionalityName: "publish" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/transfer/publish/config.vsh.yaml" functionalityNamespace: "transfer" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/transfer/publish/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/transfer/publish" set_wd_to_resources_dir: false @@ -275,6 +275,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/ingestion/cellranger_postprocessing" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/ingestion/cellranger_postprocessing/main.nf" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/workflows/ingestion/cellranger_postprocessing/main.nf b/target/nextflow/workflows/ingestion/cellranger_postprocessing/main.nf index abd8f6ae430..cf55bcdc467 100644 --- a/target/nextflow/workflows/ingestion/cellranger_postprocessing/main.nf +++ b/target/nextflow/workflows/ingestion/cellranger_postprocessing/main.nf @@ -1,4 +1,4 @@ -// cellranger_postprocessing 1.0.1 +// cellranger_postprocessing 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2786,7 +2786,7 @@ meta = [ "functionality" : { "name" : "cellranger_postprocessing", "namespace" : "workflows/ingestion", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Angela Oliveira Pisco", @@ -3016,14 +3016,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/correction/cellbender_remove_background/config.vsh.yaml", "configInfo" : { "functionalityName" : "cellbender_remove_background", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/correction/cellbender_remove_background/config.vsh.yaml", "functionalityNamespace" : "correction", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/correction/cellbender_remove_background/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/correction/cellbender_remove_background" @@ -3037,14 +3037,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/filter/filter_with_counts/config.vsh.yaml", "configInfo" : { "functionalityName" : "filter_with_counts", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/filter/filter_with_counts/config.vsh.yaml", "functionalityNamespace" : "filter", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/filter/filter_with_counts/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/filter_with_counts" @@ -3058,14 +3058,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/filter/subset_h5mu/config.vsh.yaml", "configInfo" : { "functionalityName" : "subset_h5mu", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/filter/subset_h5mu/config.vsh.yaml", "functionalityNamespace" : "filter", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/filter/subset_h5mu/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/subset_h5mu" @@ -3079,14 +3079,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/transfer/publish/config.vsh.yaml", "configInfo" : { "functionalityName" : "publish", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/transfer/publish/config.vsh.yaml", "functionalityNamespace" : "transfer", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/transfer/publish/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/transfer/publish" @@ -3153,9 +3153,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/ingestion/cellranger_postprocessing", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/workflows/ingestion/cellranger_postprocessing/nextflow.config b/target/nextflow/workflows/ingestion/cellranger_postprocessing/nextflow.config index ff778fe6806..e43fc479241 100644 --- a/target/nextflow/workflows/ingestion/cellranger_postprocessing/nextflow.config +++ b/target/nextflow/workflows/ingestion/cellranger_postprocessing/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/ingestion/cellranger_postprocessing' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Post-processing Cell Ranger datasets.' author = 'Angela Oliveira Pisco, Robrecht Cannoodt' } diff --git a/target/nextflow/workflows/ingestion/conversion/.config.vsh.yaml b/target/nextflow/workflows/ingestion/conversion/.config.vsh.yaml index 72b8a563f9b..af8024c9642 100644 --- a/target/nextflow/workflows/ingestion/conversion/.config.vsh.yaml +++ b/target/nextflow/workflows/ingestion/conversion/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "conversion" namespace: "workflows/ingestion" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -135,14 +135,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/convert/from_10xh5_to_h5mu/config.vsh.yaml" configInfo: functionalityName: "from_10xh5_to_h5mu" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/convert/from_10xh5_to_h5mu/config.vsh.yaml" functionalityNamespace: "convert" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/convert/from_10xh5_to_h5mu/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_10xh5_to_h5mu" - name: "convert/from_10xmtx_to_h5mu" @@ -152,14 +152,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/convert/from_10xmtx_to_h5mu/config.vsh.yaml" configInfo: functionalityName: "from_10xmtx_to_h5mu" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/convert/from_10xmtx_to_h5mu/config.vsh.yaml" functionalityNamespace: "convert" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/convert/from_10xmtx_to_h5mu/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_10xmtx_to_h5mu" - name: "convert/from_h5ad_to_h5mu" @@ -169,14 +169,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/convert/from_h5ad_to_h5mu/config.vsh.yaml" configInfo: functionalityName: "from_h5ad_to_h5mu" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/convert/from_h5ad_to_h5mu/config.vsh.yaml" functionalityNamespace: "convert" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/convert/from_h5ad_to_h5mu/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_h5ad_to_h5mu" set_wd_to_resources_dir: false @@ -232,6 +232,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/ingestion/conversion" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/ingestion/conversion/main.nf" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/workflows/ingestion/conversion/main.nf b/target/nextflow/workflows/ingestion/conversion/main.nf index 7a9b8ae5f91..0d4591ead8e 100644 --- a/target/nextflow/workflows/ingestion/conversion/main.nf +++ b/target/nextflow/workflows/ingestion/conversion/main.nf @@ -1,4 +1,4 @@ -// conversion 1.0.1 +// conversion 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2786,7 +2786,7 @@ meta = [ "functionality" : { "name" : "conversion", "namespace" : "workflows/ingestion", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -2979,14 +2979,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/convert/from_10xh5_to_h5mu/config.vsh.yaml", "configInfo" : { "functionalityName" : "from_10xh5_to_h5mu", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/convert/from_10xh5_to_h5mu/config.vsh.yaml", "functionalityNamespace" : "convert", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/convert/from_10xh5_to_h5mu/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_10xh5_to_h5mu" @@ -3000,14 +3000,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/convert/from_10xmtx_to_h5mu/config.vsh.yaml", "configInfo" : { "functionalityName" : "from_10xmtx_to_h5mu", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/convert/from_10xmtx_to_h5mu/config.vsh.yaml", "functionalityNamespace" : "convert", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/convert/from_10xmtx_to_h5mu/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_10xmtx_to_h5mu" @@ -3021,14 +3021,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/convert/from_h5ad_to_h5mu/config.vsh.yaml", "configInfo" : { "functionalityName" : "from_h5ad_to_h5mu", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/convert/from_h5ad_to_h5mu/config.vsh.yaml", "functionalityNamespace" : "convert", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/convert/from_h5ad_to_h5mu/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/convert/from_h5ad_to_h5mu" @@ -3095,9 +3095,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/ingestion/conversion", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/workflows/ingestion/conversion/nextflow.config b/target/nextflow/workflows/ingestion/conversion/nextflow.config index 70ff19dc845..8b1a3486b27 100644 --- a/target/nextflow/workflows/ingestion/conversion/nextflow.config +++ b/target/nextflow/workflows/ingestion/conversion/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/ingestion/conversion' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'A pipeline to convert different file formats to .h5mu.' author = 'Dries Schaumont, Dries De Maeyer' } diff --git a/target/nextflow/workflows/ingestion/demux/.config.vsh.yaml b/target/nextflow/workflows/ingestion/demux/.config.vsh.yaml index b53cbf9aad0..97e50181c65 100644 --- a/target/nextflow/workflows/ingestion/demux/.config.vsh.yaml +++ b/target/nextflow/workflows/ingestion/demux/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "demux" namespace: "workflows/ingestion" - version: "1.0.1" + version: "1.0.2" authors: - name: "Toni Verbeiren" roles: @@ -217,14 +217,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/demux/cellranger_mkfastq/config.vsh.yaml" configInfo: functionalityName: "cellranger_mkfastq" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/demux/cellranger_mkfastq/config.vsh.yaml" functionalityNamespace: "demux" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/demux/cellranger_mkfastq/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/demux/cellranger_mkfastq" - name: "demux/bcl_convert" @@ -234,14 +234,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/demux/bcl_convert/config.vsh.yaml" configInfo: functionalityName: "bcl_convert" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/demux/bcl_convert/config.vsh.yaml" functionalityNamespace: "demux" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/demux/bcl_convert/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/demux/bcl_convert" - name: "demux/bcl2fastq" @@ -251,14 +251,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/demux/bcl2fastq/config.vsh.yaml" configInfo: functionalityName: "bcl2fastq" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/demux/bcl2fastq/config.vsh.yaml" functionalityNamespace: "demux" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/demux/bcl2fastq/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/demux/bcl2fastq" - name: "qc/fastqc" @@ -268,14 +268,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/qc/fastqc/config.vsh.yaml" configInfo: functionalityName: "fastqc" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/qc/fastqc/config.vsh.yaml" functionalityNamespace: "qc" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/qc/fastqc/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/qc/fastqc" - name: "qc/multiqc" @@ -285,14 +285,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/qc/multiqc/config.vsh.yaml" configInfo: functionalityName: "multiqc" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/qc/multiqc/config.vsh.yaml" functionalityNamespace: "qc" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/qc/multiqc/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/qc/multiqc" set_wd_to_resources_dir: false @@ -348,6 +348,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/ingestion/demux" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/ingestion/demux/main.nf" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/workflows/ingestion/demux/main.nf b/target/nextflow/workflows/ingestion/demux/main.nf index 40fa82c19b8..753d6de8e32 100644 --- a/target/nextflow/workflows/ingestion/demux/main.nf +++ b/target/nextflow/workflows/ingestion/demux/main.nf @@ -1,4 +1,4 @@ -// demux 1.0.1 +// demux 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2789,7 +2789,7 @@ meta = [ "functionality" : { "name" : "demux", "namespace" : "workflows/ingestion", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Toni Verbeiren", @@ -3090,14 +3090,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/demux/cellranger_mkfastq/config.vsh.yaml", "configInfo" : { "functionalityName" : "cellranger_mkfastq", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/demux/cellranger_mkfastq/config.vsh.yaml", "functionalityNamespace" : "demux", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/demux/cellranger_mkfastq/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/demux/cellranger_mkfastq" @@ -3111,14 +3111,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/demux/bcl_convert/config.vsh.yaml", "configInfo" : { "functionalityName" : "bcl_convert", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/demux/bcl_convert/config.vsh.yaml", "functionalityNamespace" : "demux", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/demux/bcl_convert/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/demux/bcl_convert" @@ -3132,14 +3132,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/demux/bcl2fastq/config.vsh.yaml", "configInfo" : { "functionalityName" : "bcl2fastq", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/demux/bcl2fastq/config.vsh.yaml", "functionalityNamespace" : "demux", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/demux/bcl2fastq/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/demux/bcl2fastq" @@ -3153,14 +3153,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/qc/fastqc/config.vsh.yaml", "configInfo" : { "functionalityName" : "fastqc", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/qc/fastqc/config.vsh.yaml", "functionalityNamespace" : "qc", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/qc/fastqc/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/qc/fastqc" @@ -3174,14 +3174,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/qc/multiqc/config.vsh.yaml", "configInfo" : { "functionalityName" : "multiqc", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/qc/multiqc/config.vsh.yaml", "functionalityNamespace" : "qc", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/qc/multiqc/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/qc/multiqc" @@ -3248,9 +3248,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/ingestion/demux", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/workflows/ingestion/demux/nextflow.config b/target/nextflow/workflows/ingestion/demux/nextflow.config index 40f73b57608..26aa02e378c 100644 --- a/target/nextflow/workflows/ingestion/demux/nextflow.config +++ b/target/nextflow/workflows/ingestion/demux/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/ingestion/demux' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Convert `.bcl` files to `.fastq` files using bcl2fastq, bcl-convert or Cell Ranger mkfastq.\n' author = 'Toni Verbeiren, Marijke Van Moerbeke, Angela Oliveira Pisco, Samuel D\'Souza, Robrecht Cannoodt' } diff --git a/target/nextflow/workflows/ingestion/make_reference/.config.vsh.yaml b/target/nextflow/workflows/ingestion/make_reference/.config.vsh.yaml index c6463046ea6..4983fff8816 100644 --- a/target/nextflow/workflows/ingestion/make_reference/.config.vsh.yaml +++ b/target/nextflow/workflows/ingestion/make_reference/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "make_reference" namespace: "workflows/ingestion" - version: "1.0.1" + version: "1.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -220,14 +220,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/reference/make_reference/config.vsh.yaml" configInfo: functionalityName: "make_reference" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/reference/make_reference/config.vsh.yaml" functionalityNamespace: "reference" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/reference/make_reference/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/reference/make_reference" - name: "reference/build_bdrhap_reference" @@ -237,14 +237,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/reference/build_bdrhap_reference/config.vsh.yaml" configInfo: functionalityName: "build_bdrhap_reference" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/reference/build_bdrhap_reference/config.vsh.yaml" functionalityNamespace: "reference" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/reference/build_bdrhap_reference/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/reference/build_bdrhap_reference" - name: "mapping/star_build_reference" @@ -254,14 +254,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/mapping/star_build_reference/config.vsh.yml" configInfo: functionalityName: "star_build_reference" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/mapping/star_build_reference/config.vsh.yml" functionalityNamespace: "mapping" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/mapping/star_build_reference/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/star_build_reference" - name: "reference/build_cellranger_reference" @@ -271,14 +271,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/reference/build_cellranger_reference/config.vsh.yaml" configInfo: functionalityName: "build_cellranger_reference" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/reference/build_cellranger_reference/config.vsh.yaml" functionalityNamespace: "reference" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/reference/build_cellranger_reference/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/reference/build_cellranger_reference" set_wd_to_resources_dir: false @@ -334,6 +334,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/ingestion/make_reference" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/ingestion/make_reference/main.nf" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/workflows/ingestion/make_reference/main.nf b/target/nextflow/workflows/ingestion/make_reference/main.nf index 209fc520ab6..c3e3b4d0940 100644 --- a/target/nextflow/workflows/ingestion/make_reference/main.nf +++ b/target/nextflow/workflows/ingestion/make_reference/main.nf @@ -1,4 +1,4 @@ -// make_reference 1.0.1 +// make_reference 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2786,7 +2786,7 @@ meta = [ "functionality" : { "name" : "make_reference", "namespace" : "workflows/ingestion", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Angela Oliveira Pisco", @@ -3080,14 +3080,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/reference/make_reference/config.vsh.yaml", "configInfo" : { "functionalityName" : "make_reference", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/reference/make_reference/config.vsh.yaml", "functionalityNamespace" : "reference", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/reference/make_reference/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/reference/make_reference" @@ -3101,14 +3101,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/reference/build_bdrhap_reference/config.vsh.yaml", "configInfo" : { "functionalityName" : "build_bdrhap_reference", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/reference/build_bdrhap_reference/config.vsh.yaml", "functionalityNamespace" : "reference", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/reference/build_bdrhap_reference/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/reference/build_bdrhap_reference" @@ -3122,14 +3122,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/mapping/star_build_reference/config.vsh.yml", "configInfo" : { "functionalityName" : "star_build_reference", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/mapping/star_build_reference/config.vsh.yml", "functionalityNamespace" : "mapping", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/mapping/star_build_reference/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/mapping/star_build_reference" @@ -3143,14 +3143,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/reference/build_cellranger_reference/config.vsh.yaml", "configInfo" : { "functionalityName" : "build_cellranger_reference", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/reference/build_cellranger_reference/config.vsh.yaml", "functionalityNamespace" : "reference", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/reference/build_cellranger_reference/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/reference/build_cellranger_reference" @@ -3217,9 +3217,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/ingestion/make_reference", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/workflows/ingestion/make_reference/nextflow.config b/target/nextflow/workflows/ingestion/make_reference/nextflow.config index affd6432df9..98ee27a0066 100644 --- a/target/nextflow/workflows/ingestion/make_reference/nextflow.config +++ b/target/nextflow/workflows/ingestion/make_reference/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/ingestion/make_reference' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Build a transcriptomics reference into one of many formats.\n' author = 'Angela Oliveira Pisco, Robrecht Cannoodt' } diff --git a/target/nextflow/workflows/integration/bbknn_leiden/.config.vsh.yaml b/target/nextflow/workflows/integration/bbknn_leiden/.config.vsh.yaml index 98ce0b62610..4332927a108 100644 --- a/target/nextflow/workflows/integration/bbknn_leiden/.config.vsh.yaml +++ b/target/nextflow/workflows/integration/bbknn_leiden/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "bbknn_leiden" namespace: "workflows/integration" - version: "1.0.1" + version: "1.0.2" authors: - name: "Mauro Saporita" roles: @@ -272,14 +272,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/cluster/leiden/config.vsh.yaml" configInfo: functionalityName: "leiden" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/cluster/leiden/config.vsh.yaml" functionalityNamespace: "cluster" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/cluster/leiden/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/cluster/leiden" - name: "dimred/umap" @@ -289,14 +289,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/dimred/umap/config.vsh.yaml" configInfo: functionalityName: "umap" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/dimred/umap/config.vsh.yaml" functionalityNamespace: "dimred" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/dimred/umap/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/dimred/umap" - name: "neighbors/bbknn" @@ -306,14 +306,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/neighbors/bbknn/config.vsh.yaml" configInfo: functionalityName: "bbknn" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/neighbors/bbknn/config.vsh.yaml" functionalityNamespace: "neighbors" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/neighbors/bbknn/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/neighbors/bbknn" - name: "metadata/move_obsm_to_obs" @@ -323,14 +323,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/metadata/move_obsm_to_obs/config.vsh.yaml" configInfo: functionalityName: "move_obsm_to_obs" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/metadata/move_obsm_to_obs/config.vsh.yaml" functionalityNamespace: "metadata" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/metadata/move_obsm_to_obs/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/move_obsm_to_obs" set_wd_to_resources_dir: false @@ -386,6 +386,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/integration/bbknn_leiden" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/integration/bbknn_leiden/main.nf" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/workflows/integration/bbknn_leiden/main.nf b/target/nextflow/workflows/integration/bbknn_leiden/main.nf index f93f32ec1bc..df01379b8d2 100644 --- a/target/nextflow/workflows/integration/bbknn_leiden/main.nf +++ b/target/nextflow/workflows/integration/bbknn_leiden/main.nf @@ -1,4 +1,4 @@ -// bbknn_leiden 1.0.1 +// bbknn_leiden 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2786,7 +2786,7 @@ meta = [ "functionality" : { "name" : "bbknn_leiden", "namespace" : "workflows/integration", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Mauro Saporita", @@ -3129,14 +3129,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/cluster/leiden/config.vsh.yaml", "configInfo" : { "functionalityName" : "leiden", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/cluster/leiden/config.vsh.yaml", "functionalityNamespace" : "cluster", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/cluster/leiden/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/cluster/leiden" @@ -3150,14 +3150,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/dimred/umap/config.vsh.yaml", "configInfo" : { "functionalityName" : "umap", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/dimred/umap/config.vsh.yaml", "functionalityNamespace" : "dimred", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/dimred/umap/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/dimred/umap" @@ -3171,14 +3171,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/neighbors/bbknn/config.vsh.yaml", "configInfo" : { "functionalityName" : "bbknn", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/neighbors/bbknn/config.vsh.yaml", "functionalityNamespace" : "neighbors", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/neighbors/bbknn/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/neighbors/bbknn" @@ -3192,14 +3192,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/metadata/move_obsm_to_obs/config.vsh.yaml", "configInfo" : { "functionalityName" : "move_obsm_to_obs", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/metadata/move_obsm_to_obs/config.vsh.yaml", "functionalityNamespace" : "metadata", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/metadata/move_obsm_to_obs/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/move_obsm_to_obs" @@ -3266,9 +3266,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/integration/bbknn_leiden", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/workflows/integration/bbknn_leiden/nextflow.config b/target/nextflow/workflows/integration/bbknn_leiden/nextflow.config index 165f6c10e32..208f2de099c 100644 --- a/target/nextflow/workflows/integration/bbknn_leiden/nextflow.config +++ b/target/nextflow/workflows/integration/bbknn_leiden/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/integration/bbknn_leiden' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Run bbknn followed by leiden clustering and run umap on the result.' author = 'Mauro Saporita, Povilas Gibas' } diff --git a/target/nextflow/workflows/integration/harmony_leiden/.config.vsh.yaml b/target/nextflow/workflows/integration/harmony_leiden/.config.vsh.yaml index e59191cba68..680ec6a9c17 100644 --- a/target/nextflow/workflows/integration/harmony_leiden/.config.vsh.yaml +++ b/target/nextflow/workflows/integration/harmony_leiden/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "harmony_leiden" namespace: "workflows/integration" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -248,14 +248,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/cluster/leiden/config.vsh.yaml" configInfo: functionalityName: "leiden" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/cluster/leiden/config.vsh.yaml" functionalityNamespace: "cluster" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/cluster/leiden/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/cluster/leiden" - name: "integrate/harmonypy" @@ -265,14 +265,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/integrate/harmonypy/config.vsh.yaml" configInfo: functionalityName: "harmonypy" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/integrate/harmonypy/config.vsh.yaml" functionalityNamespace: "integrate" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/integrate/harmonypy/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/integrate/harmonypy" - name: "dimred/umap" @@ -282,14 +282,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/dimred/umap/config.vsh.yaml" configInfo: functionalityName: "umap" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/dimred/umap/config.vsh.yaml" functionalityNamespace: "dimred" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/dimred/umap/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/dimred/umap" - name: "neighbors/find_neighbors" @@ -299,14 +299,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/neighbors/find_neighbors/config.vsh.yaml" configInfo: functionalityName: "find_neighbors" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/neighbors/find_neighbors/config.vsh.yaml" functionalityNamespace: "neighbors" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/neighbors/find_neighbors/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/neighbors/find_neighbors" - name: "metadata/move_obsm_to_obs" @@ -316,14 +316,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/metadata/move_obsm_to_obs/config.vsh.yaml" configInfo: functionalityName: "move_obsm_to_obs" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/metadata/move_obsm_to_obs/config.vsh.yaml" functionalityNamespace: "metadata" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/metadata/move_obsm_to_obs/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/move_obsm_to_obs" set_wd_to_resources_dir: false @@ -379,6 +379,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/integration/harmony_leiden" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/integration/harmony_leiden/main.nf" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/workflows/integration/harmony_leiden/main.nf b/target/nextflow/workflows/integration/harmony_leiden/main.nf index 396da9bd92f..ecb69d4d165 100644 --- a/target/nextflow/workflows/integration/harmony_leiden/main.nf +++ b/target/nextflow/workflows/integration/harmony_leiden/main.nf @@ -1,4 +1,4 @@ -// harmony_leiden 1.0.1 +// harmony_leiden 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "harmony_leiden", "namespace" : "workflows/integration", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3104,14 +3104,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/cluster/leiden/config.vsh.yaml", "configInfo" : { "functionalityName" : "leiden", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/cluster/leiden/config.vsh.yaml", "functionalityNamespace" : "cluster", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/cluster/leiden/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/cluster/leiden" @@ -3125,14 +3125,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/integrate/harmonypy/config.vsh.yaml", "configInfo" : { "functionalityName" : "harmonypy", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/integrate/harmonypy/config.vsh.yaml", "functionalityNamespace" : "integrate", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/integrate/harmonypy/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/integrate/harmonypy" @@ -3146,14 +3146,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/dimred/umap/config.vsh.yaml", "configInfo" : { "functionalityName" : "umap", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/dimred/umap/config.vsh.yaml", "functionalityNamespace" : "dimred", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/dimred/umap/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/dimred/umap" @@ -3167,14 +3167,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/neighbors/find_neighbors/config.vsh.yaml", "configInfo" : { "functionalityName" : "find_neighbors", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/neighbors/find_neighbors/config.vsh.yaml", "functionalityNamespace" : "neighbors", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/neighbors/find_neighbors/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/neighbors/find_neighbors" @@ -3188,14 +3188,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/metadata/move_obsm_to_obs/config.vsh.yaml", "configInfo" : { "functionalityName" : "move_obsm_to_obs", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/metadata/move_obsm_to_obs/config.vsh.yaml", "functionalityNamespace" : "metadata", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/metadata/move_obsm_to_obs/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/move_obsm_to_obs" @@ -3262,9 +3262,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/integration/harmony_leiden", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/workflows/integration/harmony_leiden/nextflow.config b/target/nextflow/workflows/integration/harmony_leiden/nextflow.config index 42839166518..4e28e38d96f 100644 --- a/target/nextflow/workflows/integration/harmony_leiden/nextflow.config +++ b/target/nextflow/workflows/integration/harmony_leiden/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/integration/harmony_leiden' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Run harmony integration followed by neighbour calculations, leiden clustering and run umap on the result.' author = 'Dries Schaumont' } diff --git a/target/nextflow/workflows/integration/scanorama_leiden/.config.vsh.yaml b/target/nextflow/workflows/integration/scanorama_leiden/.config.vsh.yaml index 32e7984e683..58d49a93817 100644 --- a/target/nextflow/workflows/integration/scanorama_leiden/.config.vsh.yaml +++ b/target/nextflow/workflows/integration/scanorama_leiden/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "scanorama_leiden" namespace: "workflows/integration" - version: "1.0.1" + version: "1.0.2" authors: - name: "Mauro Saporita" roles: @@ -305,14 +305,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/cluster/leiden/config.vsh.yaml" configInfo: functionalityName: "leiden" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/cluster/leiden/config.vsh.yaml" functionalityNamespace: "cluster" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/cluster/leiden/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/cluster/leiden" - name: "integrate/scanorama" @@ -322,14 +322,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/integrate/scanorama/config.vsh.yaml" configInfo: functionalityName: "scanorama" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/integrate/scanorama/config.vsh.yaml" functionalityNamespace: "integrate" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/integrate/scanorama/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/integrate/scanorama" - name: "dimred/umap" @@ -339,14 +339,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/dimred/umap/config.vsh.yaml" configInfo: functionalityName: "umap" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/dimred/umap/config.vsh.yaml" functionalityNamespace: "dimred" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/dimred/umap/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/dimred/umap" - name: "metadata/move_obsm_to_obs" @@ -356,14 +356,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/metadata/move_obsm_to_obs/config.vsh.yaml" configInfo: functionalityName: "move_obsm_to_obs" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/metadata/move_obsm_to_obs/config.vsh.yaml" functionalityNamespace: "metadata" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/metadata/move_obsm_to_obs/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/move_obsm_to_obs" - name: "neighbors/find_neighbors" @@ -373,14 +373,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/neighbors/find_neighbors/config.vsh.yaml" configInfo: functionalityName: "find_neighbors" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/neighbors/find_neighbors/config.vsh.yaml" functionalityNamespace: "neighbors" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/neighbors/find_neighbors/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/neighbors/find_neighbors" set_wd_to_resources_dir: false @@ -436,6 +436,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/integration/scanorama_leiden" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/integration/scanorama_leiden/main.nf" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/workflows/integration/scanorama_leiden/main.nf b/target/nextflow/workflows/integration/scanorama_leiden/main.nf index 6d9031c85ad..3d12bbae25a 100644 --- a/target/nextflow/workflows/integration/scanorama_leiden/main.nf +++ b/target/nextflow/workflows/integration/scanorama_leiden/main.nf @@ -1,4 +1,4 @@ -// scanorama_leiden 1.0.1 +// scanorama_leiden 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2786,7 +2786,7 @@ meta = [ "functionality" : { "name" : "scanorama_leiden", "namespace" : "workflows/integration", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Mauro Saporita", @@ -3176,14 +3176,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/cluster/leiden/config.vsh.yaml", "configInfo" : { "functionalityName" : "leiden", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/cluster/leiden/config.vsh.yaml", "functionalityNamespace" : "cluster", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/cluster/leiden/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/cluster/leiden" @@ -3197,14 +3197,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/integrate/scanorama/config.vsh.yaml", "configInfo" : { "functionalityName" : "scanorama", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/integrate/scanorama/config.vsh.yaml", "functionalityNamespace" : "integrate", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/integrate/scanorama/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/integrate/scanorama" @@ -3218,14 +3218,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/dimred/umap/config.vsh.yaml", "configInfo" : { "functionalityName" : "umap", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/dimred/umap/config.vsh.yaml", "functionalityNamespace" : "dimred", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/dimred/umap/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/dimred/umap" @@ -3239,14 +3239,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/metadata/move_obsm_to_obs/config.vsh.yaml", "configInfo" : { "functionalityName" : "move_obsm_to_obs", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/metadata/move_obsm_to_obs/config.vsh.yaml", "functionalityNamespace" : "metadata", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/metadata/move_obsm_to_obs/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/move_obsm_to_obs" @@ -3260,14 +3260,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/neighbors/find_neighbors/config.vsh.yaml", "configInfo" : { "functionalityName" : "find_neighbors", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/neighbors/find_neighbors/config.vsh.yaml", "functionalityNamespace" : "neighbors", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/neighbors/find_neighbors/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/neighbors/find_neighbors" @@ -3334,9 +3334,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/integration/scanorama_leiden", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/workflows/integration/scanorama_leiden/nextflow.config b/target/nextflow/workflows/integration/scanorama_leiden/nextflow.config index db619d13a8b..59ca015e638 100644 --- a/target/nextflow/workflows/integration/scanorama_leiden/nextflow.config +++ b/target/nextflow/workflows/integration/scanorama_leiden/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/integration/scanorama_leiden' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Run scanorama integration followed by neighbour calculations, leiden clustering and run umap on the result.' author = 'Mauro Saporita, Povilas Gibas' } diff --git a/target/nextflow/workflows/integration/scvi_leiden/.config.vsh.yaml b/target/nextflow/workflows/integration/scvi_leiden/.config.vsh.yaml index fd7008cd2f5..bbf6b1f5077 100644 --- a/target/nextflow/workflows/integration/scvi_leiden/.config.vsh.yaml +++ b/target/nextflow/workflows/integration/scvi_leiden/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "scvi_leiden" namespace: "workflows/integration" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -338,14 +338,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/cluster/leiden/config.vsh.yaml" configInfo: functionalityName: "leiden" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/cluster/leiden/config.vsh.yaml" functionalityNamespace: "cluster" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/cluster/leiden/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/cluster/leiden" - name: "metadata/move_obsm_to_obs" @@ -355,14 +355,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/metadata/move_obsm_to_obs/config.vsh.yaml" configInfo: functionalityName: "move_obsm_to_obs" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/metadata/move_obsm_to_obs/config.vsh.yaml" functionalityNamespace: "metadata" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/metadata/move_obsm_to_obs/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/move_obsm_to_obs" - name: "integrate/scvi" @@ -372,14 +372,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/integrate/scvi/config.vsh.yaml" configInfo: functionalityName: "scvi" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/integrate/scvi/config.vsh.yaml" functionalityNamespace: "integrate" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/integrate/scvi/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/integrate/scvi" - name: "dimred/umap" @@ -389,14 +389,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/dimred/umap/config.vsh.yaml" configInfo: functionalityName: "umap" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/dimred/umap/config.vsh.yaml" functionalityNamespace: "dimred" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/dimred/umap/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/dimred/umap" - name: "neighbors/find_neighbors" @@ -406,14 +406,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/neighbors/find_neighbors/config.vsh.yaml" configInfo: functionalityName: "find_neighbors" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/neighbors/find_neighbors/config.vsh.yaml" functionalityNamespace: "neighbors" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/neighbors/find_neighbors/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/neighbors/find_neighbors" set_wd_to_resources_dir: false @@ -469,6 +469,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/integration/scvi_leiden" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/integration/scvi_leiden/main.nf" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/workflows/integration/scvi_leiden/main.nf b/target/nextflow/workflows/integration/scvi_leiden/main.nf index 8d8f11aa721..393069ab44f 100644 --- a/target/nextflow/workflows/integration/scvi_leiden/main.nf +++ b/target/nextflow/workflows/integration/scvi_leiden/main.nf @@ -1,4 +1,4 @@ -// scvi_leiden 1.0.1 +// scvi_leiden 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "scvi_leiden", "namespace" : "workflows/integration", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3199,14 +3199,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/cluster/leiden/config.vsh.yaml", "configInfo" : { "functionalityName" : "leiden", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/cluster/leiden/config.vsh.yaml", "functionalityNamespace" : "cluster", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/cluster/leiden/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/cluster/leiden" @@ -3220,14 +3220,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/metadata/move_obsm_to_obs/config.vsh.yaml", "configInfo" : { "functionalityName" : "move_obsm_to_obs", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/metadata/move_obsm_to_obs/config.vsh.yaml", "functionalityNamespace" : "metadata", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/metadata/move_obsm_to_obs/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/move_obsm_to_obs" @@ -3241,14 +3241,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/integrate/scvi/config.vsh.yaml", "configInfo" : { "functionalityName" : "scvi", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/integrate/scvi/config.vsh.yaml", "functionalityNamespace" : "integrate", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/integrate/scvi/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/integrate/scvi" @@ -3262,14 +3262,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/dimred/umap/config.vsh.yaml", "configInfo" : { "functionalityName" : "umap", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/dimred/umap/config.vsh.yaml", "functionalityNamespace" : "dimred", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/dimred/umap/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/dimred/umap" @@ -3283,14 +3283,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/neighbors/find_neighbors/config.vsh.yaml", "configInfo" : { "functionalityName" : "find_neighbors", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/neighbors/find_neighbors/config.vsh.yaml", "functionalityNamespace" : "neighbors", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/neighbors/find_neighbors/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/neighbors/find_neighbors" @@ -3357,9 +3357,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/integration/scvi_leiden", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/workflows/integration/scvi_leiden/nextflow.config b/target/nextflow/workflows/integration/scvi_leiden/nextflow.config index 3e33b5216a0..eb32ed01da1 100644 --- a/target/nextflow/workflows/integration/scvi_leiden/nextflow.config +++ b/target/nextflow/workflows/integration/scvi_leiden/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/integration/scvi_leiden' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Run scvi integration followed by neighbour calculations, leiden clustering and run umap on the result.' author = 'Dries Schaumont' } diff --git a/target/nextflow/workflows/integration/totalvi_leiden/.config.vsh.yaml b/target/nextflow/workflows/integration/totalvi_leiden/.config.vsh.yaml index 8e70f55526c..cb266d6f2f5 100644 --- a/target/nextflow/workflows/integration/totalvi_leiden/.config.vsh.yaml +++ b/target/nextflow/workflows/integration/totalvi_leiden/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "totalvi_leiden" namespace: "workflows/integration" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -422,14 +422,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/cluster/leiden/config.vsh.yaml" configInfo: functionalityName: "leiden" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/cluster/leiden/config.vsh.yaml" functionalityNamespace: "cluster" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/cluster/leiden/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/cluster/leiden" - name: "metadata/move_obsm_to_obs" @@ -439,14 +439,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/metadata/move_obsm_to_obs/config.vsh.yaml" configInfo: functionalityName: "move_obsm_to_obs" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/metadata/move_obsm_to_obs/config.vsh.yaml" functionalityNamespace: "metadata" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/metadata/move_obsm_to_obs/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/move_obsm_to_obs" - name: "integrate/totalvi" @@ -456,14 +456,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/integrate/totalvi/config.vsh.yaml" configInfo: functionalityName: "totalvi" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/integrate/totalvi/config.vsh.yaml" functionalityNamespace: "integrate" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/integrate/totalvi/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/integrate/totalvi" - name: "dimred/umap" @@ -473,14 +473,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/dimred/umap/config.vsh.yaml" configInfo: functionalityName: "umap" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/dimred/umap/config.vsh.yaml" functionalityNamespace: "dimred" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/dimred/umap/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/dimred/umap" - name: "neighbors/find_neighbors" @@ -490,14 +490,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/neighbors/find_neighbors/config.vsh.yaml" configInfo: functionalityName: "find_neighbors" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/neighbors/find_neighbors/config.vsh.yaml" functionalityNamespace: "neighbors" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/neighbors/find_neighbors/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/neighbors/find_neighbors" - name: "transfer/publish" @@ -507,14 +507,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/transfer/publish/config.vsh.yaml" configInfo: functionalityName: "publish" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/transfer/publish/config.vsh.yaml" functionalityNamespace: "transfer" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/transfer/publish/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/transfer/publish" set_wd_to_resources_dir: false @@ -570,6 +570,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/integration/totalvi_leiden" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/integration/totalvi_leiden/main.nf" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/workflows/integration/totalvi_leiden/main.nf b/target/nextflow/workflows/integration/totalvi_leiden/main.nf index 000c267f818..3c1e1065945 100644 --- a/target/nextflow/workflows/integration/totalvi_leiden/main.nf +++ b/target/nextflow/workflows/integration/totalvi_leiden/main.nf @@ -1,4 +1,4 @@ -// totalvi_leiden 1.0.1 +// totalvi_leiden 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "totalvi_leiden", "namespace" : "workflows/integration", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3307,14 +3307,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/cluster/leiden/config.vsh.yaml", "configInfo" : { "functionalityName" : "leiden", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/cluster/leiden/config.vsh.yaml", "functionalityNamespace" : "cluster", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/cluster/leiden/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/cluster/leiden" @@ -3328,14 +3328,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/metadata/move_obsm_to_obs/config.vsh.yaml", "configInfo" : { "functionalityName" : "move_obsm_to_obs", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/metadata/move_obsm_to_obs/config.vsh.yaml", "functionalityNamespace" : "metadata", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/metadata/move_obsm_to_obs/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/move_obsm_to_obs" @@ -3349,14 +3349,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/integrate/totalvi/config.vsh.yaml", "configInfo" : { "functionalityName" : "totalvi", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/integrate/totalvi/config.vsh.yaml", "functionalityNamespace" : "integrate", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/integrate/totalvi/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/integrate/totalvi" @@ -3370,14 +3370,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/dimred/umap/config.vsh.yaml", "configInfo" : { "functionalityName" : "umap", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/dimred/umap/config.vsh.yaml", "functionalityNamespace" : "dimred", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/dimred/umap/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/dimred/umap" @@ -3391,14 +3391,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/neighbors/find_neighbors/config.vsh.yaml", "configInfo" : { "functionalityName" : "find_neighbors", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/neighbors/find_neighbors/config.vsh.yaml", "functionalityNamespace" : "neighbors", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/neighbors/find_neighbors/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/neighbors/find_neighbors" @@ -3412,14 +3412,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/transfer/publish/config.vsh.yaml", "configInfo" : { "functionalityName" : "publish", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/transfer/publish/config.vsh.yaml", "functionalityNamespace" : "transfer", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/transfer/publish/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/transfer/publish" @@ -3486,9 +3486,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/integration/totalvi_leiden", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/workflows/integration/totalvi_leiden/nextflow.config b/target/nextflow/workflows/integration/totalvi_leiden/nextflow.config index a581c9e44b6..a8064a57f70 100644 --- a/target/nextflow/workflows/integration/totalvi_leiden/nextflow.config +++ b/target/nextflow/workflows/integration/totalvi_leiden/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/integration/totalvi_leiden' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Run totalVI integration followed by neighbour calculations, leiden clustering and run umap on the result.' author = 'Dries Schaumont' } diff --git a/target/nextflow/workflows/multiomics/dimensionality_reduction/.config.vsh.yaml b/target/nextflow/workflows/multiomics/dimensionality_reduction/.config.vsh.yaml index 2b48cfe2175..57234eaddb7 100644 --- a/target/nextflow/workflows/multiomics/dimensionality_reduction/.config.vsh.yaml +++ b/target/nextflow/workflows/multiomics/dimensionality_reduction/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "dimensionality_reduction" namespace: "workflows/multiomics" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -196,14 +196,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/dimred/pca/config.vsh.yaml" configInfo: functionalityName: "pca" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/dimred/pca/config.vsh.yaml" functionalityNamespace: "dimred" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/dimred/pca/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/dimred/pca" - name: "neighbors/find_neighbors" @@ -213,14 +213,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/neighbors/find_neighbors/config.vsh.yaml" configInfo: functionalityName: "find_neighbors" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/neighbors/find_neighbors/config.vsh.yaml" functionalityNamespace: "neighbors" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/neighbors/find_neighbors/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/neighbors/find_neighbors" - name: "dimred/umap" @@ -230,14 +230,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/dimred/umap/config.vsh.yaml" configInfo: functionalityName: "umap" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/dimred/umap/config.vsh.yaml" functionalityNamespace: "dimred" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/dimred/umap/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/dimred/umap" set_wd_to_resources_dir: false @@ -293,6 +293,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/multiomics/dimensionality_reduction" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/multiomics/dimensionality_reduction/main.nf" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/workflows/multiomics/dimensionality_reduction/main.nf b/target/nextflow/workflows/multiomics/dimensionality_reduction/main.nf index c772fa0bdf5..97b648cc322 100644 --- a/target/nextflow/workflows/multiomics/dimensionality_reduction/main.nf +++ b/target/nextflow/workflows/multiomics/dimensionality_reduction/main.nf @@ -1,4 +1,4 @@ -// dimensionality_reduction 1.0.1 +// dimensionality_reduction 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "dimensionality_reduction", "namespace" : "workflows/multiomics", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3043,14 +3043,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/dimred/pca/config.vsh.yaml", "configInfo" : { "functionalityName" : "pca", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/dimred/pca/config.vsh.yaml", "functionalityNamespace" : "dimred", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/dimred/pca/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/dimred/pca" @@ -3064,14 +3064,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/neighbors/find_neighbors/config.vsh.yaml", "configInfo" : { "functionalityName" : "find_neighbors", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/neighbors/find_neighbors/config.vsh.yaml", "functionalityNamespace" : "neighbors", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/neighbors/find_neighbors/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/neighbors/find_neighbors" @@ -3085,14 +3085,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/dimred/umap/config.vsh.yaml", "configInfo" : { "functionalityName" : "umap", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/dimred/umap/config.vsh.yaml", "functionalityNamespace" : "dimred", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/dimred/umap/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/dimred/umap" @@ -3159,9 +3159,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/multiomics/dimensionality_reduction", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/workflows/multiomics/dimensionality_reduction/nextflow.config b/target/nextflow/workflows/multiomics/dimensionality_reduction/nextflow.config index 28f14c2ccb0..bd93f019b30 100644 --- a/target/nextflow/workflows/multiomics/dimensionality_reduction/nextflow.config +++ b/target/nextflow/workflows/multiomics/dimensionality_reduction/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/multiomics/dimensionality_reduction' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Run calculations that output information required for most integration methods: PCA, nearest neighbour and UMAP.' author = 'Dries Schaumont' } diff --git a/target/nextflow/workflows/multiomics/process_batches/.config.vsh.yaml b/target/nextflow/workflows/multiomics/process_batches/.config.vsh.yaml index c4669b5cced..0dae2af9a76 100644 --- a/target/nextflow/workflows/multiomics/process_batches/.config.vsh.yaml +++ b/target/nextflow/workflows/multiomics/process_batches/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "process_batches" namespace: "workflows/multiomics" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -200,14 +200,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/dataflow/merge/config.vsh.yml" configInfo: functionalityName: "merge" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/dataflow/merge/config.vsh.yml" functionalityNamespace: "dataflow" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/dataflow/merge/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/dataflow/merge" - name: "workflows/multiomics/split_modalities" @@ -218,14 +218,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/workflows/multiomics/split_modalities/config.vsh.yaml" configInfo: functionalityName: "split_modalities" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/workflows/multiomics/split_modalities/config.vsh.yaml" functionalityNamespace: "workflows/multiomics" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/workflows/multiomics/split_modalities/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/multiomics/split_modalities" - name: "workflows/prot/prot_multisample" @@ -235,14 +235,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/workflows/prot/prot_multisample/config.vsh.yaml" configInfo: functionalityName: "prot_multisample" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/workflows/prot/prot_multisample/config.vsh.yaml" functionalityNamespace: "workflows/prot" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/workflows/prot/prot_multisample/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/prot/prot_multisample" - name: "workflows/rna/rna_multisample" @@ -252,14 +252,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/workflows/rna/rna_multisample/config.vsh.yaml" configInfo: functionalityName: "rna_multisample" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/workflows/rna/rna_multisample/config.vsh.yaml" functionalityNamespace: "workflows/rna" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/workflows/rna/rna_multisample/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/rna/rna_multisample" - name: "workflows/multiomics/dimensionality_reduction" @@ -270,14 +270,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/workflows/multiomics/dimensionality_reduction/config.vsh.yaml" configInfo: functionalityName: "dimensionality_reduction" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/workflows/multiomics/dimensionality_reduction/config.vsh.yaml" functionalityNamespace: "workflows/multiomics" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/workflows/multiomics/dimensionality_reduction/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/multiomics/dimensionality_reduction" - name: "workflows/multiomics/dimensionality_reduction" @@ -288,14 +288,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/workflows/multiomics/dimensionality_reduction/config.vsh.yaml" configInfo: functionalityName: "dimensionality_reduction" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/workflows/multiomics/dimensionality_reduction/config.vsh.yaml" functionalityNamespace: "workflows/multiomics" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/workflows/multiomics/dimensionality_reduction/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/multiomics/dimensionality_reduction" - name: "transfer/publish" @@ -305,14 +305,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/transfer/publish/config.vsh.yaml" configInfo: functionalityName: "publish" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/transfer/publish/config.vsh.yaml" functionalityNamespace: "transfer" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/transfer/publish/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/transfer/publish" set_wd_to_resources_dir: false @@ -368,6 +368,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/multiomics/process_batches" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/multiomics/process_batches/main.nf" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/workflows/multiomics/process_batches/main.nf b/target/nextflow/workflows/multiomics/process_batches/main.nf index 4d56dc762e5..2b57a65293e 100644 --- a/target/nextflow/workflows/multiomics/process_batches/main.nf +++ b/target/nextflow/workflows/multiomics/process_batches/main.nf @@ -1,4 +1,4 @@ -// process_batches 1.0.1 +// process_batches 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "process_batches", "namespace" : "workflows/multiomics", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3042,14 +3042,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/dataflow/merge/config.vsh.yml", "configInfo" : { "functionalityName" : "merge", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/dataflow/merge/config.vsh.yml", "functionalityNamespace" : "dataflow", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/dataflow/merge/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/dataflow/merge" @@ -3064,14 +3064,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/workflows/multiomics/split_modalities/config.vsh.yaml", "configInfo" : { "functionalityName" : "split_modalities", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/workflows/multiomics/split_modalities/config.vsh.yaml", "functionalityNamespace" : "workflows/multiomics", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/workflows/multiomics/split_modalities/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/multiomics/split_modalities" @@ -3085,14 +3085,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/workflows/prot/prot_multisample/config.vsh.yaml", "configInfo" : { "functionalityName" : "prot_multisample", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/workflows/prot/prot_multisample/config.vsh.yaml", "functionalityNamespace" : "workflows/prot", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/workflows/prot/prot_multisample/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/prot/prot_multisample" @@ -3106,14 +3106,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/workflows/rna/rna_multisample/config.vsh.yaml", "configInfo" : { "functionalityName" : "rna_multisample", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/workflows/rna/rna_multisample/config.vsh.yaml", "functionalityNamespace" : "workflows/rna", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/workflows/rna/rna_multisample/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/rna/rna_multisample" @@ -3128,14 +3128,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/workflows/multiomics/dimensionality_reduction/config.vsh.yaml", "configInfo" : { "functionalityName" : "dimensionality_reduction", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/workflows/multiomics/dimensionality_reduction/config.vsh.yaml", "functionalityNamespace" : "workflows/multiomics", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/workflows/multiomics/dimensionality_reduction/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/multiomics/dimensionality_reduction" @@ -3150,14 +3150,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/workflows/multiomics/dimensionality_reduction/config.vsh.yaml", "configInfo" : { "functionalityName" : "dimensionality_reduction", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/workflows/multiomics/dimensionality_reduction/config.vsh.yaml", "functionalityNamespace" : "workflows/multiomics", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/workflows/multiomics/dimensionality_reduction/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/multiomics/dimensionality_reduction" @@ -3171,14 +3171,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/transfer/publish/config.vsh.yaml", "configInfo" : { "functionalityName" : "publish", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/transfer/publish/config.vsh.yaml", "functionalityNamespace" : "transfer", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/transfer/publish/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/transfer/publish" @@ -3245,9 +3245,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/multiomics/process_batches", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/workflows/multiomics/process_batches/nextflow.config b/target/nextflow/workflows/multiomics/process_batches/nextflow.config index 7701584e0be..faf98116077 100644 --- a/target/nextflow/workflows/multiomics/process_batches/nextflow.config +++ b/target/nextflow/workflows/multiomics/process_batches/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/multiomics/process_batches' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'This workflow serves as an entrypoint into the \'full_pipeline\' in order to\nre-run the multisample processing and the integration setup. An input .h5mu file will \nfirst be split in order to run the multisample processing per modality. Next, the modalities\nare merged again and the integration setup pipeline is executed. Please note that this workflow\nassumes that samples from multiple pipelines are already concatenated. \n' author = 'Dries Schaumont' } diff --git a/target/nextflow/workflows/multiomics/process_samples/.config.vsh.yaml b/target/nextflow/workflows/multiomics/process_samples/.config.vsh.yaml index 8210815bdfb..b8ded48ecf5 100644 --- a/target/nextflow/workflows/multiomics/process_samples/.config.vsh.yaml +++ b/target/nextflow/workflows/multiomics/process_samples/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "process_samples" namespace: "workflows/multiomics" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -499,14 +499,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/metadata/add_id/config.vsh.yaml" configInfo: functionalityName: "add_id" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/metadata/add_id/config.vsh.yaml" functionalityNamespace: "metadata" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/metadata/add_id/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/add_id" - name: "workflows/multiomics/split_modalities" @@ -517,14 +517,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/workflows/multiomics/split_modalities/config.vsh.yaml" configInfo: functionalityName: "split_modalities" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/workflows/multiomics/split_modalities/config.vsh.yaml" functionalityNamespace: "workflows/multiomics" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/workflows/multiomics/split_modalities/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/multiomics/split_modalities" - name: "dataflow/merge" @@ -534,14 +534,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/dataflow/merge/config.vsh.yml" configInfo: functionalityName: "merge" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/dataflow/merge/config.vsh.yml" functionalityNamespace: "dataflow" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/dataflow/merge/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/dataflow/merge" - name: "dataflow/concatenate_h5mu" @@ -551,14 +551,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/dataflow/concatenate_h5mu/config.vsh.yaml" configInfo: functionalityName: "concatenate_h5mu" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/dataflow/concatenate_h5mu/config.vsh.yaml" functionalityNamespace: "dataflow" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/dataflow/concatenate_h5mu/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/dataflow/concatenate_h5mu" - name: "transfer/publish" @@ -568,14 +568,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/transfer/publish/config.vsh.yaml" configInfo: functionalityName: "publish" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/transfer/publish/config.vsh.yaml" functionalityNamespace: "transfer" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/transfer/publish/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/transfer/publish" - name: "workflows/rna/rna_singlesample" @@ -585,14 +585,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/workflows/rna/rna_singlesample/config.vsh.yaml" configInfo: functionalityName: "rna_singlesample" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/workflows/rna/rna_singlesample/config.vsh.yaml" functionalityNamespace: "workflows/rna" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/workflows/rna/rna_singlesample/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/rna/rna_singlesample" - name: "workflows/prot/prot_singlesample" @@ -602,14 +602,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/workflows/prot/prot_singlesample/config.vsh.yaml" configInfo: functionalityName: "prot_singlesample" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/workflows/prot/prot_singlesample/config.vsh.yaml" functionalityNamespace: "workflows/prot" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/workflows/prot/prot_singlesample/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/prot/prot_singlesample" - name: "workflows/gdo/gdo_singlesample" @@ -619,14 +619,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/workflows/gdo/gdo_singlesample/config.vsh.yaml" configInfo: functionalityName: "gdo_singlesample" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/workflows/gdo/gdo_singlesample/config.vsh.yaml" functionalityNamespace: "workflows/gdo" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/workflows/gdo/gdo_singlesample/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/gdo/gdo_singlesample" - name: "workflows/multiomics/process_batches" @@ -636,14 +636,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/workflows/multiomics/process_batches/config.vsh.yaml" configInfo: functionalityName: "process_batches" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/workflows/multiomics/process_batches/config.vsh.yaml" functionalityNamespace: "workflows/multiomics" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/workflows/multiomics/process_batches/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/multiomics/process_batches" set_wd_to_resources_dir: false @@ -699,6 +699,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/multiomics/process_samples" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/multiomics/process_samples/main.nf" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/workflows/multiomics/process_samples/main.nf b/target/nextflow/workflows/multiomics/process_samples/main.nf index 66777bd81cb..1cb6b57ff82 100644 --- a/target/nextflow/workflows/multiomics/process_samples/main.nf +++ b/target/nextflow/workflows/multiomics/process_samples/main.nf @@ -1,4 +1,4 @@ -// process_samples 1.0.1 +// process_samples 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "process_samples", "namespace" : "workflows/multiomics", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3407,14 +3407,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/metadata/add_id/config.vsh.yaml", "configInfo" : { "functionalityName" : "add_id", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/metadata/add_id/config.vsh.yaml", "functionalityNamespace" : "metadata", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/metadata/add_id/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/add_id" @@ -3429,14 +3429,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/workflows/multiomics/split_modalities/config.vsh.yaml", "configInfo" : { "functionalityName" : "split_modalities", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/workflows/multiomics/split_modalities/config.vsh.yaml", "functionalityNamespace" : "workflows/multiomics", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/workflows/multiomics/split_modalities/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/multiomics/split_modalities" @@ -3450,14 +3450,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/dataflow/merge/config.vsh.yml", "configInfo" : { "functionalityName" : "merge", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/dataflow/merge/config.vsh.yml", "functionalityNamespace" : "dataflow", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/dataflow/merge/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/dataflow/merge" @@ -3471,14 +3471,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/dataflow/concatenate_h5mu/config.vsh.yaml", "configInfo" : { "functionalityName" : "concatenate_h5mu", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/dataflow/concatenate_h5mu/config.vsh.yaml", "functionalityNamespace" : "dataflow", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/dataflow/concatenate_h5mu/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/dataflow/concatenate_h5mu" @@ -3492,14 +3492,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/transfer/publish/config.vsh.yaml", "configInfo" : { "functionalityName" : "publish", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/transfer/publish/config.vsh.yaml", "functionalityNamespace" : "transfer", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/transfer/publish/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/transfer/publish" @@ -3513,14 +3513,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/workflows/rna/rna_singlesample/config.vsh.yaml", "configInfo" : { "functionalityName" : "rna_singlesample", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/workflows/rna/rna_singlesample/config.vsh.yaml", "functionalityNamespace" : "workflows/rna", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/workflows/rna/rna_singlesample/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/rna/rna_singlesample" @@ -3534,14 +3534,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/workflows/prot/prot_singlesample/config.vsh.yaml", "configInfo" : { "functionalityName" : "prot_singlesample", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/workflows/prot/prot_singlesample/config.vsh.yaml", "functionalityNamespace" : "workflows/prot", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/workflows/prot/prot_singlesample/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/prot/prot_singlesample" @@ -3555,14 +3555,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/workflows/gdo/gdo_singlesample/config.vsh.yaml", "configInfo" : { "functionalityName" : "gdo_singlesample", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/workflows/gdo/gdo_singlesample/config.vsh.yaml", "functionalityNamespace" : "workflows/gdo", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/workflows/gdo/gdo_singlesample/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/gdo/gdo_singlesample" @@ -3576,14 +3576,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/workflows/multiomics/process_batches/config.vsh.yaml", "configInfo" : { "functionalityName" : "process_batches", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/workflows/multiomics/process_batches/config.vsh.yaml", "functionalityNamespace" : "workflows/multiomics", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/workflows/multiomics/process_batches/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/multiomics/process_batches" @@ -3650,9 +3650,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/multiomics/process_samples", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/workflows/multiomics/process_samples/nextflow.config b/target/nextflow/workflows/multiomics/process_samples/nextflow.config index 4abb1c4e991..de3b72c847b 100644 --- a/target/nextflow/workflows/multiomics/process_samples/nextflow.config +++ b/target/nextflow/workflows/multiomics/process_samples/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/multiomics/process_samples' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'A pipeline to analyse multiple multiomics samples.' author = 'Dries Schaumont' } diff --git a/target/nextflow/workflows/multiomics/split_modalities/.config.vsh.yaml b/target/nextflow/workflows/multiomics/split_modalities/.config.vsh.yaml index 5027c36d380..ad09468a2be 100644 --- a/target/nextflow/workflows/multiomics/split_modalities/.config.vsh.yaml +++ b/target/nextflow/workflows/multiomics/split_modalities/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "split_modalities" namespace: "workflows/multiomics" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -108,14 +108,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/dataflow/split_modalities/config.vsh.yaml" configInfo: functionalityName: "split_modalities" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/dataflow/split_modalities/config.vsh.yaml" functionalityNamespace: "dataflow" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/dataflow/split_modalities/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/dataflow/split_modalities" set_wd_to_resources_dir: false @@ -171,6 +171,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/multiomics/split_modalities" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/multiomics/split_modalities/main.nf" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/workflows/multiomics/split_modalities/main.nf b/target/nextflow/workflows/multiomics/split_modalities/main.nf index 363e1864524..f4e91ac2661 100644 --- a/target/nextflow/workflows/multiomics/split_modalities/main.nf +++ b/target/nextflow/workflows/multiomics/split_modalities/main.nf @@ -1,4 +1,4 @@ -// split_modalities 1.0.1 +// split_modalities 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "split_modalities", "namespace" : "workflows/multiomics", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -2931,14 +2931,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/dataflow/split_modalities/config.vsh.yaml", "configInfo" : { "functionalityName" : "split_modalities", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/dataflow/split_modalities/config.vsh.yaml", "functionalityNamespace" : "dataflow", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/dataflow/split_modalities/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/dataflow/split_modalities" @@ -3005,9 +3005,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/multiomics/split_modalities", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/workflows/multiomics/split_modalities/nextflow.config b/target/nextflow/workflows/multiomics/split_modalities/nextflow.config index 2c9055083dc..cb1c2d568b4 100644 --- a/target/nextflow/workflows/multiomics/split_modalities/nextflow.config +++ b/target/nextflow/workflows/multiomics/split_modalities/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/multiomics/split_modalities' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'A pipeline to split a multimodal mudata files into several unimodal mudata files.' author = 'Dries Schaumont' } diff --git a/target/nextflow/workflows/prot/prot_multisample/.config.vsh.yaml b/target/nextflow/workflows/prot/prot_multisample/.config.vsh.yaml index 9139463597e..305c35925a3 100644 --- a/target/nextflow/workflows/prot/prot_multisample/.config.vsh.yaml +++ b/target/nextflow/workflows/prot/prot_multisample/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "prot_multisample" namespace: "workflows/prot" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -211,14 +211,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/transform/clr/config.vsh.yaml" configInfo: functionalityName: "clr" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/transform/clr/config.vsh.yaml" functionalityNamespace: "transform" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/transform/clr/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/clr" - name: "workflows/qc/qc" @@ -229,14 +229,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/workflows/qc/qc/config.vsh.yaml" configInfo: functionalityName: "qc" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/workflows/qc/qc/config.vsh.yaml" functionalityNamespace: "workflows/qc" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/workflows/qc/qc/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/qc/qc" set_wd_to_resources_dir: false @@ -292,6 +292,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/prot/prot_multisample" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/prot/prot_multisample/main.nf" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/workflows/prot/prot_multisample/main.nf b/target/nextflow/workflows/prot/prot_multisample/main.nf index 0112c7619e7..e1e7002c142 100644 --- a/target/nextflow/workflows/prot/prot_multisample/main.nf +++ b/target/nextflow/workflows/prot/prot_multisample/main.nf @@ -1,4 +1,4 @@ -// prot_multisample 1.0.1 +// prot_multisample 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "prot_multisample", "namespace" : "workflows/prot", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3045,14 +3045,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/transform/clr/config.vsh.yaml", "configInfo" : { "functionalityName" : "clr", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/transform/clr/config.vsh.yaml", "functionalityNamespace" : "transform", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/transform/clr/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/clr" @@ -3067,14 +3067,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/workflows/qc/qc/config.vsh.yaml", "configInfo" : { "functionalityName" : "qc", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/workflows/qc/qc/config.vsh.yaml", "functionalityNamespace" : "workflows/qc", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/workflows/qc/qc/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/qc/qc" @@ -3141,9 +3141,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/prot/prot_multisample", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/workflows/prot/prot_multisample/nextflow.config b/target/nextflow/workflows/prot/prot_multisample/nextflow.config index 27ecaab382d..eb6620d14f8 100644 --- a/target/nextflow/workflows/prot/prot_multisample/nextflow.config +++ b/target/nextflow/workflows/prot/prot_multisample/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/prot/prot_multisample' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Processing unimodal multi-sample ADT data.' author = 'Dries Schaumont' } diff --git a/target/nextflow/workflows/prot/prot_singlesample/.config.vsh.yaml b/target/nextflow/workflows/prot/prot_singlesample/.config.vsh.yaml index 0685d181c88..d7d861c032c 100644 --- a/target/nextflow/workflows/prot/prot_singlesample/.config.vsh.yaml +++ b/target/nextflow/workflows/prot/prot_singlesample/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "prot_singlesample" namespace: "workflows/prot" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries De Maeyer" roles: @@ -191,14 +191,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/filter/filter_with_counts/config.vsh.yaml" configInfo: functionalityName: "filter_with_counts" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/filter/filter_with_counts/config.vsh.yaml" functionalityNamespace: "filter" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/filter/filter_with_counts/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/filter_with_counts" - name: "filter/do_filter" @@ -208,14 +208,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/filter/do_filter/config.vsh.yaml" configInfo: functionalityName: "do_filter" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/filter/do_filter/config.vsh.yaml" functionalityNamespace: "filter" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/filter/do_filter/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/do_filter" set_wd_to_resources_dir: false @@ -271,6 +271,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/prot/prot_singlesample" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/prot/prot_singlesample/main.nf" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/workflows/prot/prot_singlesample/main.nf b/target/nextflow/workflows/prot/prot_singlesample/main.nf index 37b1e526e26..4319da702a5 100644 --- a/target/nextflow/workflows/prot/prot_singlesample/main.nf +++ b/target/nextflow/workflows/prot/prot_singlesample/main.nf @@ -1,4 +1,4 @@ -// prot_singlesample 1.0.1 +// prot_singlesample 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2787,7 +2787,7 @@ meta = [ "functionality" : { "name" : "prot_singlesample", "namespace" : "workflows/prot", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries De Maeyer", @@ -3054,14 +3054,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/filter/filter_with_counts/config.vsh.yaml", "configInfo" : { "functionalityName" : "filter_with_counts", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/filter/filter_with_counts/config.vsh.yaml", "functionalityNamespace" : "filter", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/filter/filter_with_counts/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/filter_with_counts" @@ -3075,14 +3075,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/filter/do_filter/config.vsh.yaml", "configInfo" : { "functionalityName" : "do_filter", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/filter/do_filter/config.vsh.yaml", "functionalityNamespace" : "filter", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/filter/do_filter/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/do_filter" @@ -3149,9 +3149,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/prot/prot_singlesample", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/workflows/prot/prot_singlesample/nextflow.config b/target/nextflow/workflows/prot/prot_singlesample/nextflow.config index 44941011e91..c52e4f6f4c6 100644 --- a/target/nextflow/workflows/prot/prot_singlesample/nextflow.config +++ b/target/nextflow/workflows/prot/prot_singlesample/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/prot/prot_singlesample' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Processing unimodal single-sample CITE-seq data.' author = 'Dries De Maeyer, Robrecht Cannoodt, Dries Schaumont' } diff --git a/target/nextflow/workflows/qc/qc/.config.vsh.yaml b/target/nextflow/workflows/qc/qc/.config.vsh.yaml index fa961856d83..6f55742595e 100644 --- a/target/nextflow/workflows/qc/qc/.config.vsh.yaml +++ b/target/nextflow/workflows/qc/qc/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "qc" namespace: "workflows/qc" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries Schaumont" roles: @@ -276,14 +276,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/transfer/publish/config.vsh.yaml" configInfo: functionalityName: "publish" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/transfer/publish/config.vsh.yaml" functionalityNamespace: "transfer" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/transfer/publish/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/transfer/publish" - name: "metadata/grep_annotation_column" @@ -293,14 +293,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/metadata/grep_annotation_column/config.vsh.yaml" configInfo: functionalityName: "grep_annotation_column" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/metadata/grep_annotation_column/config.vsh.yaml" functionalityNamespace: "metadata" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/metadata/grep_annotation_column/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/grep_annotation_column" - name: "qc/calculate_qc_metrics" @@ -310,14 +310,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/qc/calculate_qc_metrics/config.vsh.yaml" configInfo: functionalityName: "calculate_qc_metrics" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/qc/calculate_qc_metrics/config.vsh.yaml" functionalityNamespace: "qc" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/qc/calculate_qc_metrics/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/qc/calculate_qc_metrics" set_wd_to_resources_dir: false @@ -373,6 +373,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/qc/qc" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/qc/qc/main.nf" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/workflows/qc/qc/main.nf b/target/nextflow/workflows/qc/qc/main.nf index d782579d228..9a7296b878c 100644 --- a/target/nextflow/workflows/qc/qc/main.nf +++ b/target/nextflow/workflows/qc/qc/main.nf @@ -1,4 +1,4 @@ -// qc 1.0.1 +// qc 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2785,7 +2785,7 @@ meta = [ "functionality" : { "name" : "qc", "namespace" : "workflows/qc", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3118,14 +3118,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/transfer/publish/config.vsh.yaml", "configInfo" : { "functionalityName" : "publish", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/transfer/publish/config.vsh.yaml", "functionalityNamespace" : "transfer", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/transfer/publish/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/transfer/publish" @@ -3139,14 +3139,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/metadata/grep_annotation_column/config.vsh.yaml", "configInfo" : { "functionalityName" : "grep_annotation_column", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/metadata/grep_annotation_column/config.vsh.yaml", "functionalityNamespace" : "metadata", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/metadata/grep_annotation_column/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/grep_annotation_column" @@ -3160,14 +3160,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/qc/calculate_qc_metrics/config.vsh.yaml", "configInfo" : { "functionalityName" : "calculate_qc_metrics", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/qc/calculate_qc_metrics/config.vsh.yaml", "functionalityNamespace" : "qc", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/qc/calculate_qc_metrics/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/qc/calculate_qc_metrics" @@ -3234,9 +3234,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/qc/qc", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/workflows/qc/qc/nextflow.config b/target/nextflow/workflows/qc/qc/nextflow.config index 6a4b8cdba8c..3e9cd9610e4 100644 --- a/target/nextflow/workflows/qc/qc/nextflow.config +++ b/target/nextflow/workflows/qc/qc/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/qc/qc' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'A pipeline to add basic qc statistics to a MuData ' author = 'Dries Schaumont' } diff --git a/target/nextflow/workflows/rna/rna_multisample/.config.vsh.yaml b/target/nextflow/workflows/rna/rna_multisample/.config.vsh.yaml index 78772f52989..97e84b5ae28 100644 --- a/target/nextflow/workflows/rna/rna_multisample/.config.vsh.yaml +++ b/target/nextflow/workflows/rna/rna_multisample/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "rna_multisample" namespace: "workflows/rna" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries De Maeyer" roles: @@ -321,14 +321,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/transform/normalize_total/config.vsh.yaml" configInfo: functionalityName: "normalize_total" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/transform/normalize_total/config.vsh.yaml" functionalityNamespace: "transform" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/transform/normalize_total/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/normalize_total" - name: "transform/log1p" @@ -338,14 +338,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/transform/log1p/config.vsh.yaml" configInfo: functionalityName: "log1p" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/transform/log1p/config.vsh.yaml" functionalityNamespace: "transform" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/transform/log1p/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/log1p" - name: "feature_annotation/highly_variable_features_scanpy" @@ -355,14 +355,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/feature_annotation/highly_variable_features_scanpy/config.vsh.yaml" configInfo: functionalityName: "highly_variable_features_scanpy" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/feature_annotation/highly_variable_features_scanpy/config.vsh.yaml" functionalityNamespace: "feature_annotation" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/feature_annotation/highly_variable_features_scanpy/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/feature_annotation/highly_variable_features_scanpy" - name: "workflows/qc/qc" @@ -373,14 +373,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/workflows/qc/qc/config.vsh.yaml" configInfo: functionalityName: "qc" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/workflows/qc/qc/config.vsh.yaml" functionalityNamespace: "workflows/qc" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/workflows/qc/qc/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/qc/qc" - name: "transform/delete_layer" @@ -390,14 +390,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/transform/delete_layer/config.vsh.yaml" configInfo: functionalityName: "delete_layer" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/transform/delete_layer/config.vsh.yaml" functionalityNamespace: "transform" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/transform/delete_layer/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/delete_layer" - name: "metadata/add_id" @@ -407,14 +407,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/metadata/add_id/config.vsh.yaml" configInfo: functionalityName: "add_id" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/metadata/add_id/config.vsh.yaml" functionalityNamespace: "metadata" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/metadata/add_id/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/add_id" set_wd_to_resources_dir: false @@ -470,6 +470,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/rna/rna_multisample" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/rna/rna_multisample/main.nf" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/workflows/rna/rna_multisample/main.nf b/target/nextflow/workflows/rna/rna_multisample/main.nf index d3317f73be3..a4400caf9ce 100644 --- a/target/nextflow/workflows/rna/rna_multisample/main.nf +++ b/target/nextflow/workflows/rna/rna_multisample/main.nf @@ -1,4 +1,4 @@ -// rna_multisample 1.0.1 +// rna_multisample 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2787,7 +2787,7 @@ meta = [ "functionality" : { "name" : "rna_multisample", "namespace" : "workflows/rna", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries De Maeyer", @@ -3183,14 +3183,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/transform/normalize_total/config.vsh.yaml", "configInfo" : { "functionalityName" : "normalize_total", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/transform/normalize_total/config.vsh.yaml", "functionalityNamespace" : "transform", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/transform/normalize_total/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/normalize_total" @@ -3204,14 +3204,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/transform/log1p/config.vsh.yaml", "configInfo" : { "functionalityName" : "log1p", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/transform/log1p/config.vsh.yaml", "functionalityNamespace" : "transform", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/transform/log1p/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/log1p" @@ -3225,14 +3225,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/feature_annotation/highly_variable_features_scanpy/config.vsh.yaml", "configInfo" : { "functionalityName" : "highly_variable_features_scanpy", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/feature_annotation/highly_variable_features_scanpy/config.vsh.yaml", "functionalityNamespace" : "feature_annotation", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/feature_annotation/highly_variable_features_scanpy/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/feature_annotation/highly_variable_features_scanpy" @@ -3247,14 +3247,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/workflows/qc/qc/config.vsh.yaml", "configInfo" : { "functionalityName" : "qc", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/workflows/qc/qc/config.vsh.yaml", "functionalityNamespace" : "workflows/qc", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/workflows/qc/qc/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/qc/qc" @@ -3268,14 +3268,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/transform/delete_layer/config.vsh.yaml", "configInfo" : { "functionalityName" : "delete_layer", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/transform/delete_layer/config.vsh.yaml", "functionalityNamespace" : "transform", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/transform/delete_layer/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/transform/delete_layer" @@ -3289,14 +3289,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/metadata/add_id/config.vsh.yaml", "configInfo" : { "functionalityName" : "add_id", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/metadata/add_id/config.vsh.yaml", "functionalityNamespace" : "metadata", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/metadata/add_id/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/metadata/add_id" @@ -3363,9 +3363,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/rna/rna_multisample", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/workflows/rna/rna_multisample/nextflow.config b/target/nextflow/workflows/rna/rna_multisample/nextflow.config index 9a44ab33caa..14f73c6ff49 100644 --- a/target/nextflow/workflows/rna/rna_multisample/nextflow.config +++ b/target/nextflow/workflows/rna/rna_multisample/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/rna/rna_multisample' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Processing unimodal multi-sample RNA transcriptomics data.' author = 'Dries De Maeyer, Robrecht Cannoodt, Dries Schaumont' } diff --git a/target/nextflow/workflows/rna/rna_singlesample/.config.vsh.yaml b/target/nextflow/workflows/rna/rna_singlesample/.config.vsh.yaml index 34332825121..0ebf98411e0 100644 --- a/target/nextflow/workflows/rna/rna_singlesample/.config.vsh.yaml +++ b/target/nextflow/workflows/rna/rna_singlesample/.config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "rna_singlesample" namespace: "workflows/rna" - version: "1.0.1" + version: "1.0.2" authors: - name: "Dries De Maeyer" roles: @@ -270,14 +270,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/filter/filter_with_counts/config.vsh.yaml" configInfo: functionalityName: "filter_with_counts" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/filter/filter_with_counts/config.vsh.yaml" functionalityNamespace: "filter" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/filter/filter_with_counts/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/filter_with_counts" - name: "filter/filter_with_scrublet" @@ -287,14 +287,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/filter/filter_with_scrublet/config.vsh.yaml" configInfo: functionalityName: "filter_with_scrublet" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/filter/filter_with_scrublet/config.vsh.yaml" functionalityNamespace: "filter" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/filter/filter_with_scrublet/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/filter_with_scrublet" - name: "filter/do_filter" @@ -304,14 +304,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/filter/do_filter/config.vsh.yaml" configInfo: functionalityName: "do_filter" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/filter/do_filter/config.vsh.yaml" functionalityNamespace: "filter" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/filter/do_filter/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/do_filter" - name: "filter/delimit_fraction" @@ -321,14 +321,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/filter/delimit_fraction/config.vsh.yaml" configInfo: functionalityName: "delimit_fraction" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/filter/delimit_fraction/config.vsh.yaml" functionalityNamespace: "filter" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/filter/delimit_fraction/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/delimit_fraction" - name: "workflows/qc/qc" @@ -338,14 +338,14 @@ functionality: foundConfigPath: "/home/runner/work/openpipeline/openpipeline/src/workflows/qc/qc/config.vsh.yaml" configInfo: functionalityName: "qc" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" git_remote: "https://github.com/openpipelines-bio/openpipeline" viash_version: "0.8.6" config: "/home/runner/work/openpipeline/openpipeline/src/workflows/qc/qc/config.vsh.yaml" functionalityNamespace: "workflows/qc" output: "" platform: "" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" executable: "/nextflow/workflows/qc/qc/main.nf" writtenPath: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/qc/qc" set_wd_to_resources_dir: false @@ -401,6 +401,6 @@ info: output: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/rna/rna_singlesample" executable: "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/rna/rna_singlesample/main.nf" viash_version: "0.8.6" - git_commit: "8ba584e550ac93c484a8b6ddea0c44618d02cf3f" + git_commit: "57add3ff137ac44d67bc7456cb9146bc6dc633cc" git_remote: "https://github.com/openpipelines-bio/openpipeline" - git_tag: "1.0.0-1-g8ba584e550" + git_tag: "1.0.1-3-g57add3ff13" diff --git a/target/nextflow/workflows/rna/rna_singlesample/main.nf b/target/nextflow/workflows/rna/rna_singlesample/main.nf index 30e20b8e642..0f1558755bf 100644 --- a/target/nextflow/workflows/rna/rna_singlesample/main.nf +++ b/target/nextflow/workflows/rna/rna_singlesample/main.nf @@ -1,4 +1,4 @@ -// rna_singlesample 1.0.1 +// rna_singlesample 1.0.2 // // This wrapper script is auto-generated by viash 0.8.6 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2787,7 +2787,7 @@ meta = [ "functionality" : { "name" : "rna_singlesample", "namespace" : "workflows/rna", - "version" : "1.0.1", + "version" : "1.0.2", "authors" : [ { "name" : "Dries De Maeyer", @@ -3142,14 +3142,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/filter/filter_with_counts/config.vsh.yaml", "configInfo" : { "functionalityName" : "filter_with_counts", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/filter/filter_with_counts/config.vsh.yaml", "functionalityNamespace" : "filter", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/filter/filter_with_counts/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/filter_with_counts" @@ -3163,14 +3163,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/filter/filter_with_scrublet/config.vsh.yaml", "configInfo" : { "functionalityName" : "filter_with_scrublet", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/filter/filter_with_scrublet/config.vsh.yaml", "functionalityNamespace" : "filter", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/filter/filter_with_scrublet/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/filter_with_scrublet" @@ -3184,14 +3184,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/filter/do_filter/config.vsh.yaml", "configInfo" : { "functionalityName" : "do_filter", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/filter/do_filter/config.vsh.yaml", "functionalityNamespace" : "filter", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/filter/do_filter/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/do_filter" @@ -3205,14 +3205,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/filter/delimit_fraction/config.vsh.yaml", "configInfo" : { "functionalityName" : "delimit_fraction", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/filter/delimit_fraction/config.vsh.yaml", "functionalityNamespace" : "filter", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/filter/delimit_fraction/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/filter/delimit_fraction" @@ -3226,14 +3226,14 @@ meta = [ "foundConfigPath" : "/home/runner/work/openpipeline/openpipeline/src/workflows/qc/qc/config.vsh.yaml", "configInfo" : { "functionalityName" : "qc", - "git_tag" : "1.0.0-1-g8ba584e550", + "git_tag" : "1.0.1-3-g57add3ff13", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", "viash_version" : "0.8.6", "config" : "/home/runner/work/openpipeline/openpipeline/src/workflows/qc/qc/config.vsh.yaml", "functionalityNamespace" : "workflows/qc", "output" : "", "platform" : "", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "executable" : "/nextflow/workflows/qc/qc/main.nf" }, "writtenPath" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/qc/qc" @@ -3300,9 +3300,9 @@ meta = [ "platform" : "nextflow", "output" : "/home/runner/work/openpipeline/openpipeline/target/nextflow/workflows/rna/rna_singlesample", "viash_version" : "0.8.6", - "git_commit" : "8ba584e550ac93c484a8b6ddea0c44618d02cf3f", + "git_commit" : "57add3ff137ac44d67bc7456cb9146bc6dc633cc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline", - "git_tag" : "1.0.0-1-g8ba584e550" + "git_tag" : "1.0.1-3-g57add3ff13" } }''')) ] diff --git a/target/nextflow/workflows/rna/rna_singlesample/nextflow.config b/target/nextflow/workflows/rna/rna_singlesample/nextflow.config index 22fce9af17e..61bd0925d75 100644 --- a/target/nextflow/workflows/rna/rna_singlesample/nextflow.config +++ b/target/nextflow/workflows/rna/rna_singlesample/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/rna/rna_singlesample' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = '1.0.1' + version = '1.0.2' description = 'Processing unimodal single-sample RNA transcriptomics data.' author = 'Dries De Maeyer, Robrecht Cannoodt, Dries Schaumont' }