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Merge pull request #887 from openpipelines-bio/add_metrics #1092

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Job	Run time
Build and push target folder	5m 58s
Build and Deploy Docker Images (celltypist, /, annotate, src/annotate/celltypist/config.vsh.yaml,...	3m 43s
Build and Deploy Docker Images (onclass, /, annotate, src/annotate/onclass/config.vsh.yaml, src/a...	18m 0s
Build and Deploy Docker Images (popv, /, annotate, src/annotate/popv/config.vsh.yaml, src/annotat...	14m 4s
Build and Deploy Docker Images (random_forest_annotation, /, annotate, src/annotate/random_forest...	3m 6s
Build and Deploy Docker Images (scanvi, /, annotate, src/annotate/scanvi/config.vsh.yaml, src/ann...	9m 38s
Build and Deploy Docker Images (svm_annotation, /, annotate, src/annotate/svm_annotation/config.v...	2m 55s
Build and Deploy Docker Images (leiden, /, cluster, src/cluster/leiden/config.vsh.yaml, src/clust...	1m 54s
Build and Deploy Docker Images (compress_h5mu, /, compression, src/compression/compress_h5mu/conf...	2m 13s
Build and Deploy Docker Images (tar_extract, /, compression, src/compression/tar_extract/config.v...	56s
Build and Deploy Docker Images (from_10xh5_to_h5mu, /, convert, src/convert/from_10xh5_to_h5mu/co...	2m 26s
Build and Deploy Docker Images (from_10xmtx_to_h5mu, /, convert, src/convert/from_10xmtx_to_h5mu/...	3m 49s
Build and Deploy Docker Images (from_bd_to_10x_molecular_barcode_tags, /, convert, src/convert/fr...	2m 10s
Build and Deploy Docker Images (from_bdrhap_to_h5mu, /, convert, src/convert/from_bdrhap_to_h5mu/...	1m 24s
Build and Deploy Docker Images (from_cellranger_multi_to_h5mu, /, convert, src/convert/from_cellr...	1m 52s
Build and Deploy Docker Images (from_h5ad_to_h5mu, /, convert, src/convert/from_h5ad_to_h5mu/conf...	1m 20s
Build and Deploy Docker Images (from_h5mu_to_h5ad, /, convert, src/convert/from_h5mu_to_h5ad/conf...	1m 19s
Build and Deploy Docker Images (from_h5mu_to_seurat, /, convert, src/convert/from_h5mu_to_seurat/...	3m 33s
Build and Deploy Docker Images (cellbender_remove_background, /, correction, src/correction/cellb...	9m 57s
Build and Deploy Docker Images (cellbender_remove_background_v0_2, /, correction, src/correction/...	5m 50s
Build and Deploy Docker Images (concatenate_h5mu, /, dataflow, src/dataflow/concatenate_h5mu/conf...	3m 13s
Build and Deploy Docker Images (merge, /, dataflow, src/dataflow/merge/config.vsh.yml, src/datafl...	1m 44s
Build and Deploy Docker Images (split_h5mu, /, dataflow, src/dataflow/split_h5mu/config.vsh.yaml,...	2m 45s
Build and Deploy Docker Images (split_h5mu_train_test, /, dataflow, src/dataflow/split_h5mu_train...	2m 16s
Build and Deploy Docker Images (split_modalities, /, dataflow, src/dataflow/split_modalities/conf...	2m 50s
Build and Deploy Docker Images (bcl2fastq, /, demux, src/demux/bcl2fastq/config.vsh.yaml, src/dem...	5m 37s
Build and Deploy Docker Images (bcl_convert, /, demux, src/demux/bcl_convert/config.vsh.yaml, src...	1m 18s
Build and Deploy Docker Images (cellranger_atac_mkfastq, /, demux, src/demux/cellranger_atac_mkfa...	1m 10s
Build and Deploy Docker Images (cellranger_mkfastq, /, demux, src/demux/cellranger_mkfastq/config...	2m 39s
Build and Deploy Docker Images (densmap, /, dimred, src/dimred/densmap/config.vsh.yaml, src/dimre...	3m 49s
Build and Deploy Docker Images (lsi, /, dimred, src/dimred/lsi/config.vsh.yaml, src/dimred/lsi/)	2m 32s
Build and Deploy Docker Images (pca, /, dimred, src/dimred/pca/config.vsh.yaml, src/dimred/pca/)	2m 5s
Build and Deploy Docker Images (tsne, /, dimred, src/dimred/tsne/config.vsh.yaml, src/dimred/tsne/)	3m 42s
Build and Deploy Docker Images (umap, /, dimred, src/dimred/umap/config.vsh.yaml, src/dimred/umap/)	8m 7s
Build and Deploy Docker Images (download_file, /, download, src/download/download_file/config.vsh...	50s
Build and Deploy Docker Images (sync_test_resources, /, download, src/download/sync_test_resource...	2m 23s
Build and Deploy Docker Images (highly_variable_features_scanpy, /, feature_annotation, src/featu...	2m 28s
Build and Deploy Docker Images (score_genes_cell_cycle_scanpy, /, feature_annotation, src/feature...	3m 10s
Build and Deploy Docker Images (score_genes_scanpy, /, feature_annotation, src/feature_annotation...	2m 0s
Build and Deploy Docker Images (make_params, /, files, src/files/make_params/config.vsh.yaml, src...	1m 32s
Build and Deploy Docker Images (delimit_fraction, /, filter, src/filter/delimit_fraction/config.v...	1m 33s
Build and Deploy Docker Images (do_filter, /, filter, src/filter/do_filter/config.vsh.yaml, src/f...	2m 52s
Build and Deploy Docker Images (filter_with_counts, /, filter, src/filter/filter_with_counts/conf...	1m 19s
Build and Deploy Docker Images (filter_with_scrublet, /, filter, src/filter/filter_with_scrublet/...	2m 24s
Build and Deploy Docker Images (intersect_obs, /, filter, src/filter/intersect_obs/config.vsh.yam...	3m 5s
Build and Deploy Docker Images (remove_modality, /, filter, src/filter/remove_modality/config.vsh...	1m 20s
Build and Deploy Docker Images (subset_h5mu, /, filter, src/filter/subset_h5mu/config.vsh.yaml, s...	1m 21s
Build and Deploy Docker Images (bcftools, /, genetic_demux, src/genetic_demux/bcftools/config.vsh...	2m 46s
Build and Deploy Docker Images (cellsnp, /, genetic_demux, src/genetic_demux/cellsnp/config.vsh.y...	4m 13s
Build and Deploy Docker Images (demuxlet, /, genetic_demux, src/genetic_demux/demuxlet/config.vsh...	7m 21s
Build and Deploy Docker Images (dsc_pileup, /, genetic_demux, src/genetic_demux/dsc_pileup/config...	4m 8s
Build and Deploy Docker Images (freebayes, /, genetic_demux, src/genetic_demux/freebayes/config.v...	1m 39s
Build and Deploy Docker Images (freemuxlet, /, genetic_demux, src/genetic_demux/freemuxlet/config...	9m 14s
Build and Deploy Docker Images (samtools, /, genetic_demux, src/genetic_demux/samtools/config.vsh...	3m 52s
Build and Deploy Docker Images (scsplit, /, genetic_demux, src/genetic_demux/scsplit/config.vsh.y...	2m 16s
Build and Deploy Docker Images (souporcell, /, genetic_demux, src/genetic_demux/souporcell/config...	4m 22s
Build and Deploy Docker Images (vireo, /, genetic_demux, src/genetic_demux/vireo/config.vsh.yaml,...	1m 31s
Build and Deploy Docker Images (harmonypy, /, integrate, src/integrate/harmonypy/config.vsh.yaml,...	1m 50s
Build and Deploy Docker Images (scanorama, /, integrate, src/integrate/scanorama/config.vsh.yaml,...	2m 27s
Build and Deploy Docker Images (scarches, /, integrate, src/integrate/scarches/config.vsh.yaml, s...	14m 45s
Build and Deploy Docker Images (scvi, /, integrate, src/integrate/scvi/config.vsh.yaml, src/integ...	12m 11s
Build and Deploy Docker Images (totalvi, /, integrate, src/integrate/totalvi/config.vsh.yaml, src...	15m 22s
Build and Deploy Docker Images (lianapy, /, interpret, src/interpret/lianapy/config.vsh.yaml, src...	8m 59s
Build and Deploy Docker Images (pynndescent_knn, /, labels_transfer, src/labels_transfer/pynndesc...	1m 36s
Build and Deploy Docker Images (xgboost, /, labels_transfer, src/labels_transfer/xgboost/config.v...	2m 13s
Build and Deploy Docker Images (bd_rhapsody, /, mapping, src/mapping/bd_rhapsody/config.vsh.yaml,...	1m 55s
Build and Deploy Docker Images (cellranger_atac_count, /, mapping, src/mapping/cellranger_atac_co...	3m 5s
Build and Deploy Docker Images (cellranger_count, /, mapping, src/mapping/cellranger_count/config...	3m 8s
Build and Deploy Docker Images (cellranger_count_split, /, mapping, src/mapping/cellranger_count_...	2m 18s
Build and Deploy Docker Images (cellranger_multi, /, mapping, src/mapping/cellranger_multi/config...	1m 38s
Build and Deploy Docker Images (htseq_count, /, mapping, src/mapping/htseq_count/config.vsh.yaml,...	1m 22s
Build and Deploy Docker Images (htseq_count_to_h5mu, /, mapping, src/mapping/htseq_count_to_h5mu/...	4m 17s
Build and Deploy Docker Images (multi_star, /, mapping, src/mapping/multi_star/config.vsh.yaml, s...	5m 53s
Build and Deploy Docker Images (multi_star_to_h5mu, /, mapping, src/mapping/multi_star_to_h5mu/co...	2m 38s
Build and Deploy Docker Images (samtools_sort, /, mapping, src/mapping/samtools_sort/config.vsh.y...	1m 6s
Build and Deploy Docker Images (star_align, /, mapping, src/mapping/star_align/config.vsh.yaml, s...	6m 23s
Build and Deploy Docker Images (star_align_v273a, /, mapping, src/mapping/star_align_v273a/config...	2m 58s
Build and Deploy Docker Images (add_id, /, metadata, src/metadata/add_id/config.vsh.yaml, src/met...	1m 56s
Build and Deploy Docker Images (copy_obs, /, metadata, src/metadata/copy_obs/config.vsh.yaml, src...	1m 31s
Build and Deploy Docker Images (duplicate_var, /, metadata, src/metadata/duplicate_var/config.vsh...	1m 20s
Build and Deploy Docker Images (grep_annotation_column, /, metadata, src/metadata/grep_annotation...	3m 6s
Build and Deploy Docker Images (join_csv, /, metadata, src/metadata/join_csv/config.vsh.yml, src/...	1m 23s
Build and Deploy Docker Images (join_uns_to_obs, /, metadata, src/metadata/join_uns_to_obs/config...	1m 21s
Build and Deploy Docker Images (move_obsm_to_obs, /, metadata, src/metadata/move_obsm_to_obs/conf...	1m 26s
Build and Deploy Docker Images (bbknn, /, neighbors, src/neighbors/bbknn/config.vsh.yaml, src/nei...	2m 41s
Build and Deploy Docker Images (find_neighbors, /, neighbors, src/neighbors/find_neighbors/config...	1m 46s
Build and Deploy Docker Images (filter_10xh5, /, process_10xh5, src/process_10xh5/filter_10xh5/co...	4m 3s
Build and Deploy Docker Images (calculate_qc_metrics, /, qc, src/qc/calculate_qc_metrics/config.v...	1m 24s
Build and Deploy Docker Images (fastqc, /, qc, src/qc/fastqc/config.vsh.yaml, src/qc/fastqc/)	1m 36s
Build and Deploy Docker Images (multiqc, /, qc, src/qc/multiqc/config.vsh.yaml, src/qc/multiqc/)	1m 58s
Build and Deploy Docker Images (cellxgene_census, /, query, src/query/cellxgene_census/config.vsh...	11m 19s
Build and Deploy Docker Images (build_bdrhap_reference, /, reference, src/reference/build_bdrhap_...	1m 50s
Build and Deploy Docker Images (build_cellranger_arc_reference, /, reference, src/reference/build...	2m 22s
Build and Deploy Docker Images (build_cellranger_reference, /, reference, src/reference/build_cel...	1m 38s
Build and Deploy Docker Images (build_star_reference, /, reference, src/reference/build_star_refe...	3m 56s
Build and Deploy Docker Images (cellranger_mkgtf, /, reference, src/reference/cellranger_mkgtf/co...	1m 21s
Build and Deploy Docker Images (make_reference, /, reference, src/reference/make_reference/config...	1m 0s
Build and Deploy Docker Images (mermaid, /, report, src/report/mermaid/config.vsh.yaml, src/repor...	4m 56s
Build and Deploy Docker Images (binning, /, scgpt, src/scgpt/binning/config.vsh.yaml, src/scgpt/b...	2m 19s
Build and Deploy Docker Images (cell_type_annotation, /, scgpt, src/scgpt/cell_type_annotation/co...	7m 7s
Build and Deploy Docker Images (cross_check_genes, /, scgpt, src/scgpt/cross_check_genes/config.v...	5m 51s
Build and Deploy Docker Images (embedding, /, scgpt, src/scgpt/embedding/config.vsh.yaml, src/scg...	7m 15s
Build and Deploy Docker Images (pad_tokenize, /, scgpt, src/scgpt/pad_tokenize/config.vsh.yaml, s...	7m 41s
Build and Deploy Docker Images (publish, /, transfer, src/transfer/publish/config.vsh.yaml, src/t...	2m 36s
Build and Deploy Docker Images (bpcells_regress_out, /, transform, src/transform/bpcells_regress_...	8m 58s
Build and Deploy Docker Images (clr, /, transform, src/transform/clr/config.vsh.yaml, src/transfo...	1m 42s
Build and Deploy Docker Images (delete_layer, /, transform, src/transform/delete_layer/config.vsh...	1m 35s
Build and Deploy Docker Images (log1p, /, transform, src/transform/log1p/config.vsh.yaml, src/tra...	5m 21s
Build and Deploy Docker Images (move_layer, /, transform, src/transform/move_layer/config.vsh.yam...	3m 16s
Build and Deploy Docker Images (normalize_total, /, transform, src/transform/normalize_total/conf...	4m 18s
Build and Deploy Docker Images (regress_out, /, transform, src/transform/regress_out/config.vsh.y...	3m 47s
Build and Deploy Docker Images (scale, /, transform, src/transform/scale/config.vsh.yaml, src/tra...	2m 30s
Build and Deploy Docker Images (tfidf, /, transform, src/transform/tfidf/config.vsh.yaml, src/tra...	4m 26s
Build and Deploy Docker Images (scvelo, /, velocity, src/velocity/scvelo/config.vsh.yaml, src/vel...	15m 42s
Build and Deploy Docker Images (velocyto, /, velocity, src/velocity/velocyto/config.vsh.yaml, src...	8m 4s
Build and Deploy Docker Images (velocyto_to_h5mu, /, convert, src/velocity/velocyto_to_h5mu/confi...	1m 54s
Build and Deploy Docker Images (bd_rhapsody_test, /, test_workflows/ingestion, src/workflows/test...	1m 38s
Build and Deploy Docker Images (cellranger_mapping_test, /, test_workflows/ingestion, src/workflo...	1m 24s
Build and Deploy Docker Images (cellranger_multi_test, /, test_workflows/ingestion, src/workflows...	2m 44s
Build and Deploy Docker Images (cellranger_postprocessing_test, /, test_workflows/ingestion, src/...	1m 24s
Build and Deploy Docker Images (conversion_test, /, test_workflows/ingestion, src/workflows/test_...	3m 4s
Build and Deploy Docker Images (dimensionality_reduction_test, /, test_workflows/multiomics, src/...	1m 50s
Build and Deploy Docker Images (workflow_test, /, test_workflows/multiomics/process_batches, src/...	1m 30s
Build and Deploy Docker Images (workflow_test2, /, test_workflows/multiomics/process_batches, src...	1m 53s
Build and Deploy Docker Images (split_modalities_test, /, test_workflows/multiomics, src/workflow...	1m 48s
Build and Deploy Docker Images (qc_test, /, test_workflows/qc, src/workflows/test_workflows/qc/co...	1m 32s
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Merge pull request #887 from openpipelines-bio/add_metrics #1092

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Merge pull request #887 from openpipelines-bio/add_metrics #1092

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