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Deploy for release 0.1.3 from 1c80b24
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rcannood committed May 31, 2023
1 parent 0086f7a commit ebc700c
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Showing 35 changed files with 42 additions and 42 deletions.
4 changes: 2 additions & 2 deletions scripts/README.md
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Expand Up @@ -74,7 +74,7 @@ viash run src/operations/create_runner_script/config.vsh.yaml -- \
--repository czbiohub/utilities \
--main_script src/mapping/process_10x/main.nf \
--entry auto \
--revision 0.1.2 \
--revision 0.1.3 \
--singularity_cache_dir /hpc/scratch/group.data.science/singularity_images \
--tower_workspace_id 124983787544228 \
--nextflow_config /hpc/scratch/group.data.science/utilities/scripts/czbhpc.config
Expand All @@ -84,7 +84,7 @@ viash run src/operations/create_runner_script/config.vsh.yaml -- \
--repository czbiohub/utilities \
--main_script src/mapping/process_smartseq2/main.nf \
--entry auto \
--revision 0.1.2 \
--revision 0.1.3 \
--singularity_cache_dir /hpc/scratch/group.data.science/singularity_images \
--tower_workspace_id 124983787544228 \
--nextflow_config /hpc/scratch/group.data.science/utilities/scripts/czbhpc.config
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2 changes: 1 addition & 1 deletion scripts/process_10x
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@@ -1,7 +1,7 @@

#!/bin/bash

UTILITIES_TAG="${UTILITIES_TAG:-0.1.2}"
UTILITIES_TAG="${UTILITIES_TAG:-0.1.3}"

set -e

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2 changes: 1 addition & 1 deletion scripts/process_smartseq2
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@@ -1,7 +1,7 @@

#!/bin/bash

UTILITIES_TAG="${UTILITIES_TAG:-0.1.2}"
UTILITIES_TAG="${UTILITIES_TAG:-0.1.3}"

set -e

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2 changes: 1 addition & 1 deletion target/docker/demux/spaceranger_mkfastq/.config.vsh.yaml
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Expand Up @@ -79,5 +79,5 @@ info:
output: "/home/runner/work/utilities/utilities/target/docker/demux/spaceranger_mkfastq"
executable: "/home/runner/work/utilities/utilities/target/docker/demux/spaceranger_mkfastq/spaceranger_mkfastq"
viash_version: "0.7.3"
git_commit: "0120a8e813499e4a6c690a375ba663aea07fca8a"
git_commit: "1c80b24785f7ee036cd00534f1d36a6c9d9855b7"
git_remote: "https://github.com/czbiohub/utilities"
4 changes: 2 additions & 2 deletions target/docker/demux/spaceranger_mkfastq/spaceranger_mkfastq
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Expand Up @@ -399,9 +399,9 @@ FROM ghcr.io/data-intuitive/spaceranger:latest
RUN :
LABEL org.opencontainers.image.description="Companion container for running component demux spaceranger_mkfastq"
LABEL org.opencontainers.image.created="2023-05-31T19:00:36Z"
LABEL org.opencontainers.image.created="2023-05-31T19:23:28Z"
LABEL org.opencontainers.image.source="https://github.com/czbiohub/utilities"
LABEL org.opencontainers.image.revision="0120a8e813499e4a6c690a375ba663aea07fca8a"
LABEL org.opencontainers.image.revision="1c80b24785f7ee036cd00534f1d36a6c9d9855b7"
LABEL org.opencontainers.image.version="0.1.3"
VIASHDOCKER
}
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2 changes: 1 addition & 1 deletion target/docker/mapping/spaceranger_count/.config.vsh.yaml
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Expand Up @@ -129,5 +129,5 @@ info:
output: "/home/runner/work/utilities/utilities/target/docker/mapping/spaceranger_count"
executable: "/home/runner/work/utilities/utilities/target/docker/mapping/spaceranger_count/spaceranger_count"
viash_version: "0.7.3"
git_commit: "0120a8e813499e4a6c690a375ba663aea07fca8a"
git_commit: "1c80b24785f7ee036cd00534f1d36a6c9d9855b7"
git_remote: "https://github.com/czbiohub/utilities"
4 changes: 2 additions & 2 deletions target/docker/mapping/spaceranger_count/spaceranger_count
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Expand Up @@ -423,9 +423,9 @@ FROM ghcr.io/data-intuitive/spaceranger:latest
RUN :
LABEL org.opencontainers.image.description="Companion container for running component mapping spaceranger_count"
LABEL org.opencontainers.image.created="2023-05-31T19:00:37Z"
LABEL org.opencontainers.image.created="2023-05-31T19:23:28Z"
LABEL org.opencontainers.image.source="https://github.com/czbiohub/utilities"
LABEL org.opencontainers.image.revision="0120a8e813499e4a6c690a375ba663aea07fca8a"
LABEL org.opencontainers.image.revision="1c80b24785f7ee036cd00534f1d36a6c9d9855b7"
LABEL org.opencontainers.image.version="0.1.3"
VIASHDOCKER
}
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Expand Up @@ -105,5 +105,5 @@ info:
output: "/home/runner/work/utilities/utilities/target/docker/multiomics/cellranger_arc_aggr"
executable: "/home/runner/work/utilities/utilities/target/docker/multiomics/cellranger_arc_aggr/cellranger_arc_aggr"
viash_version: "0.7.3"
git_commit: "0120a8e813499e4a6c690a375ba663aea07fca8a"
git_commit: "1c80b24785f7ee036cd00534f1d36a6c9d9855b7"
git_remote: "https://github.com/czbiohub/utilities"
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Expand Up @@ -418,9 +418,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "numpy" "pandas" "scanpy"
LABEL org.opencontainers.image.description="Companion container for running component multiomics cellranger_arc_aggr"
LABEL org.opencontainers.image.created="2023-05-31T19:00:36Z"
LABEL org.opencontainers.image.created="2023-05-31T19:23:29Z"
LABEL org.opencontainers.image.source="https://github.com/czbiohub/utilities"
LABEL org.opencontainers.image.revision="0120a8e813499e4a6c690a375ba663aea07fca8a"
LABEL org.opencontainers.image.revision="1c80b24785f7ee036cd00534f1d36a6c9d9855b7"
LABEL org.opencontainers.image.version="0.1.3"
VIASHDOCKER
}
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Expand Up @@ -97,5 +97,5 @@ info:
output: "/home/runner/work/utilities/utilities/target/docker/multiomics/cellranger_arc_count"
executable: "/home/runner/work/utilities/utilities/target/docker/multiomics/cellranger_arc_count/cellranger_arc_count"
viash_version: "0.7.3"
git_commit: "0120a8e813499e4a6c690a375ba663aea07fca8a"
git_commit: "1c80b24785f7ee036cd00534f1d36a6c9d9855b7"
git_remote: "https://github.com/czbiohub/utilities"
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Expand Up @@ -416,9 +416,9 @@ FROM ghcr.io/data-intuitive/cellranger_arc:2.0
RUN :
LABEL org.opencontainers.image.description="Companion container for running component multiomics cellranger_arc_count"
LABEL org.opencontainers.image.created="2023-05-31T19:00:36Z"
LABEL org.opencontainers.image.created="2023-05-31T19:23:28Z"
LABEL org.opencontainers.image.source="https://github.com/czbiohub/utilities"
LABEL org.opencontainers.image.revision="0120a8e813499e4a6c690a375ba663aea07fca8a"
LABEL org.opencontainers.image.revision="1c80b24785f7ee036cd00534f1d36a6c9d9855b7"
LABEL org.opencontainers.image.version="0.1.3"
VIASHDOCKER
}
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Expand Up @@ -95,5 +95,5 @@ info:
output: "/home/runner/work/utilities/utilities/target/docker/multiomics/cellranger_cite_seq"
executable: "/home/runner/work/utilities/utilities/target/docker/multiomics/cellranger_cite_seq/cellranger_cite_seq"
viash_version: "0.7.3"
git_commit: "0120a8e813499e4a6c690a375ba663aea07fca8a"
git_commit: "1c80b24785f7ee036cd00534f1d36a6c9d9855b7"
git_remote: "https://github.com/czbiohub/utilities"
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Expand Up @@ -409,9 +409,9 @@ FROM ghcr.io/data-intuitive/cellranger_arc:2.0
RUN :
LABEL org.opencontainers.image.description="Companion container for running component multiomics cellranger_cite_seq"
LABEL org.opencontainers.image.created="2023-05-31T19:00:37Z"
LABEL org.opencontainers.image.created="2023-05-31T19:23:28Z"
LABEL org.opencontainers.image.source="https://github.com/czbiohub/utilities"
LABEL org.opencontainers.image.revision="0120a8e813499e4a6c690a375ba663aea07fca8a"
LABEL org.opencontainers.image.revision="1c80b24785f7ee036cd00534f1d36a6c9d9855b7"
LABEL org.opencontainers.image.version="0.1.3"
VIASHDOCKER
}
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Expand Up @@ -122,5 +122,5 @@ info:
output: "/home/runner/work/utilities/utilities/target/docker/operations/create_runner_script"
executable: "/home/runner/work/utilities/utilities/target/docker/operations/create_runner_script/create_runner_script"
viash_version: "0.7.3"
git_commit: "0120a8e813499e4a6c690a375ba663aea07fca8a"
git_commit: "1c80b24785f7ee036cd00534f1d36a6c9d9855b7"
git_remote: "https://github.com/czbiohub/utilities"
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Expand Up @@ -426,9 +426,9 @@ FROM python:3.10
RUN :
LABEL org.opencontainers.image.description="Companion container for running component operations create_runner_script"
LABEL org.opencontainers.image.created="2023-05-31T19:00:36Z"
LABEL org.opencontainers.image.created="2023-05-31T19:23:28Z"
LABEL org.opencontainers.image.source="https://github.com/czbiohub/utilities"
LABEL org.opencontainers.image.revision="0120a8e813499e4a6c690a375ba663aea07fca8a"
LABEL org.opencontainers.image.revision="1c80b24785f7ee036cd00534f1d36a6c9d9855b7"
LABEL org.opencontainers.image.version="0.1.3"
VIASHDOCKER
}
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2 changes: 1 addition & 1 deletion target/native/demux/spaceranger_mkfastq/.config.vsh.yaml
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Expand Up @@ -79,5 +79,5 @@ info:
output: "/home/runner/work/utilities/utilities/target/native/demux/spaceranger_mkfastq"
executable: "/home/runner/work/utilities/utilities/target/native/demux/spaceranger_mkfastq/spaceranger_mkfastq"
viash_version: "0.7.3"
git_commit: "0120a8e813499e4a6c690a375ba663aea07fca8a"
git_commit: "1c80b24785f7ee036cd00534f1d36a6c9d9855b7"
git_remote: "https://github.com/czbiohub/utilities"
2 changes: 1 addition & 1 deletion target/native/mapping/spaceranger_count/.config.vsh.yaml
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Expand Up @@ -129,5 +129,5 @@ info:
output: "/home/runner/work/utilities/utilities/target/native/mapping/spaceranger_count"
executable: "/home/runner/work/utilities/utilities/target/native/mapping/spaceranger_count/spaceranger_count"
viash_version: "0.7.3"
git_commit: "0120a8e813499e4a6c690a375ba663aea07fca8a"
git_commit: "1c80b24785f7ee036cd00534f1d36a6c9d9855b7"
git_remote: "https://github.com/czbiohub/utilities"
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Expand Up @@ -105,5 +105,5 @@ info:
output: "/home/runner/work/utilities/utilities/target/native/multiomics/cellranger_arc_aggr"
executable: "/home/runner/work/utilities/utilities/target/native/multiomics/cellranger_arc_aggr/cellranger_arc_aggr"
viash_version: "0.7.3"
git_commit: "0120a8e813499e4a6c690a375ba663aea07fca8a"
git_commit: "1c80b24785f7ee036cd00534f1d36a6c9d9855b7"
git_remote: "https://github.com/czbiohub/utilities"
Original file line number Diff line number Diff line change
Expand Up @@ -97,5 +97,5 @@ info:
output: "/home/runner/work/utilities/utilities/target/native/multiomics/cellranger_arc_count"
executable: "/home/runner/work/utilities/utilities/target/native/multiomics/cellranger_arc_count/cellranger_arc_count"
viash_version: "0.7.3"
git_commit: "0120a8e813499e4a6c690a375ba663aea07fca8a"
git_commit: "1c80b24785f7ee036cd00534f1d36a6c9d9855b7"
git_remote: "https://github.com/czbiohub/utilities"
Original file line number Diff line number Diff line change
Expand Up @@ -95,5 +95,5 @@ info:
output: "/home/runner/work/utilities/utilities/target/native/multiomics/cellranger_cite_seq"
executable: "/home/runner/work/utilities/utilities/target/native/multiomics/cellranger_cite_seq/cellranger_cite_seq"
viash_version: "0.7.3"
git_commit: "0120a8e813499e4a6c690a375ba663aea07fca8a"
git_commit: "1c80b24785f7ee036cd00534f1d36a6c9d9855b7"
git_remote: "https://github.com/czbiohub/utilities"
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Expand Up @@ -122,5 +122,5 @@ info:
output: "/home/runner/work/utilities/utilities/target/native/operations/create_runner_script"
executable: "/home/runner/work/utilities/utilities/target/native/operations/create_runner_script/create_runner_script"
viash_version: "0.7.3"
git_commit: "0120a8e813499e4a6c690a375ba663aea07fca8a"
git_commit: "1c80b24785f7ee036cd00534f1d36a6c9d9855b7"
git_remote: "https://github.com/czbiohub/utilities"
2 changes: 1 addition & 1 deletion target/nextflow/demux/spaceranger_mkfastq/.config.vsh.yaml
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Expand Up @@ -79,5 +79,5 @@ info:
output: "/home/runner/work/utilities/utilities/target/nextflow/demux/spaceranger_mkfastq"
executable: "/home/runner/work/utilities/utilities/target/nextflow/demux/spaceranger_mkfastq/spaceranger_mkfastq"
viash_version: "0.7.3"
git_commit: "0120a8e813499e4a6c690a375ba663aea07fca8a"
git_commit: "1c80b24785f7ee036cd00534f1d36a6c9d9855b7"
git_remote: "https://github.com/czbiohub/utilities"
2 changes: 1 addition & 1 deletion target/nextflow/demux/spaceranger_mkfastq/main.nf
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Expand Up @@ -123,7 +123,7 @@ thisConfig = processConfig(jsonSlurper.parseText('''{
"config" : "/home/runner/work/utilities/utilities/src/demux/spaceranger_mkfastq/config.vsh.yaml",
"platform" : "nextflow",
"viash_version" : "0.7.3",
"git_commit" : "0120a8e813499e4a6c690a375ba663aea07fca8a",
"git_commit" : "1c80b24785f7ee036cd00534f1d36a6c9d9855b7",
"git_remote" : "https://github.com/czbiohub/utilities"
}
}'''))
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2 changes: 1 addition & 1 deletion target/nextflow/mapping/process_10x/.config.vsh.yaml
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Expand Up @@ -105,5 +105,5 @@ info:
output: "/home/runner/work/utilities/utilities/target/nextflow/mapping/process_10x"
executable: "/home/runner/work/utilities/utilities/target/nextflow/mapping/process_10x/process_10x"
viash_version: "0.7.3"
git_commit: "0120a8e813499e4a6c690a375ba663aea07fca8a"
git_commit: "1c80b24785f7ee036cd00534f1d36a6c9d9855b7"
git_remote: "https://github.com/czbiohub/utilities"
2 changes: 1 addition & 1 deletion target/nextflow/mapping/process_10x/main.nf
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Expand Up @@ -168,7 +168,7 @@ thisConfig = processConfig(jsonSlurper.parseText('''{
"config" : "/home/runner/work/utilities/utilities/src/mapping/process_10x/config.vsh.yaml",
"platform" : "nextflow",
"viash_version" : "0.7.3",
"git_commit" : "0120a8e813499e4a6c690a375ba663aea07fca8a",
"git_commit" : "1c80b24785f7ee036cd00534f1d36a6c9d9855b7",
"git_remote" : "https://github.com/czbiohub/utilities"
}
}'''))
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2 changes: 1 addition & 1 deletion target/nextflow/mapping/process_10x_auto/.config.vsh.yaml
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Expand Up @@ -150,5 +150,5 @@ info:
output: "/home/runner/work/utilities/utilities/target/nextflow/mapping/process_10x_auto"
executable: "/home/runner/work/utilities/utilities/target/nextflow/mapping/process_10x_auto/process_10x_auto"
viash_version: "0.7.3"
git_commit: "0120a8e813499e4a6c690a375ba663aea07fca8a"
git_commit: "1c80b24785f7ee036cd00534f1d36a6c9d9855b7"
git_remote: "https://github.com/czbiohub/utilities"
2 changes: 1 addition & 1 deletion target/nextflow/mapping/process_10x_auto/main.nf
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Expand Up @@ -208,7 +208,7 @@ thisConfig = processConfig(jsonSlurper.parseText('''{
"config" : "/home/runner/work/utilities/utilities/src/mapping/process_10x/auto.vsh.yaml",
"platform" : "nextflow",
"viash_version" : "0.7.3",
"git_commit" : "0120a8e813499e4a6c690a375ba663aea07fca8a",
"git_commit" : "1c80b24785f7ee036cd00534f1d36a6c9d9855b7",
"git_remote" : "https://github.com/czbiohub/utilities"
}
}'''))
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2 changes: 1 addition & 1 deletion target/nextflow/mapping/process_smartseq2/.config.vsh.yaml
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Expand Up @@ -146,5 +146,5 @@ info:
output: "/home/runner/work/utilities/utilities/target/nextflow/mapping/process_smartseq2"
executable: "/home/runner/work/utilities/utilities/target/nextflow/mapping/process_smartseq2/process_smartseq2"
viash_version: "0.7.3"
git_commit: "0120a8e813499e4a6c690a375ba663aea07fca8a"
git_commit: "1c80b24785f7ee036cd00534f1d36a6c9d9855b7"
git_remote: "https://github.com/czbiohub/utilities"
2 changes: 1 addition & 1 deletion target/nextflow/mapping/process_smartseq2/main.nf
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Expand Up @@ -216,7 +216,7 @@ thisConfig = processConfig(jsonSlurper.parseText('''{
"config" : "/home/runner/work/utilities/utilities/src/mapping/process_smartseq2/config.vsh.yaml",
"platform" : "nextflow",
"viash_version" : "0.7.3",
"git_commit" : "0120a8e813499e4a6c690a375ba663aea07fca8a",
"git_commit" : "1c80b24785f7ee036cd00534f1d36a6c9d9855b7",
"git_remote" : "https://github.com/czbiohub/utilities"
}
}'''))
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Original file line number Diff line number Diff line change
Expand Up @@ -178,5 +178,5 @@ info:
output: "/home/runner/work/utilities/utilities/target/nextflow/mapping/process_smartseq2_auto"
executable: "/home/runner/work/utilities/utilities/target/nextflow/mapping/process_smartseq2_auto/process_smartseq2_auto"
viash_version: "0.7.3"
git_commit: "0120a8e813499e4a6c690a375ba663aea07fca8a"
git_commit: "1c80b24785f7ee036cd00534f1d36a6c9d9855b7"
git_remote: "https://github.com/czbiohub/utilities"
2 changes: 1 addition & 1 deletion target/nextflow/mapping/process_smartseq2_auto/main.nf
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Expand Up @@ -242,7 +242,7 @@ thisConfig = processConfig(jsonSlurper.parseText('''{
"config" : "/home/runner/work/utilities/utilities/src/mapping/process_smartseq2/auto.vsh.yaml",
"platform" : "nextflow",
"viash_version" : "0.7.3",
"git_commit" : "0120a8e813499e4a6c690a375ba663aea07fca8a",
"git_commit" : "1c80b24785f7ee036cd00534f1d36a6c9d9855b7",
"git_remote" : "https://github.com/czbiohub/utilities"
}
}'''))
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2 changes: 1 addition & 1 deletion target/nextflow/mapping/spaceranger_count/.config.vsh.yaml
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Expand Up @@ -129,5 +129,5 @@ info:
output: "/home/runner/work/utilities/utilities/target/nextflow/mapping/spaceranger_count"
executable: "/home/runner/work/utilities/utilities/target/nextflow/mapping/spaceranger_count/spaceranger_count"
viash_version: "0.7.3"
git_commit: "0120a8e813499e4a6c690a375ba663aea07fca8a"
git_commit: "1c80b24785f7ee036cd00534f1d36a6c9d9855b7"
git_remote: "https://github.com/czbiohub/utilities"
2 changes: 1 addition & 1 deletion target/nextflow/mapping/spaceranger_count/main.nf
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Expand Up @@ -187,7 +187,7 @@ thisConfig = processConfig(jsonSlurper.parseText('''{
"config" : "/home/runner/work/utilities/utilities/src/mapping/spaceranger_count/config.vsh.yaml",
"platform" : "nextflow",
"viash_version" : "0.7.3",
"git_commit" : "0120a8e813499e4a6c690a375ba663aea07fca8a",
"git_commit" : "1c80b24785f7ee036cd00534f1d36a6c9d9855b7",
"git_remote" : "https://github.com/czbiohub/utilities"
}
}'''))
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2 changes: 1 addition & 1 deletion target/nextflow/tabula_sapiens/concat/.config.vsh.yaml
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Expand Up @@ -92,5 +92,5 @@ info:
output: "/home/runner/work/utilities/utilities/target/nextflow/tabula_sapiens/concat"
executable: "/home/runner/work/utilities/utilities/target/nextflow/tabula_sapiens/concat/concat"
viash_version: "0.7.3"
git_commit: "0120a8e813499e4a6c690a375ba663aea07fca8a"
git_commit: "1c80b24785f7ee036cd00534f1d36a6c9d9855b7"
git_remote: "https://github.com/czbiohub/utilities"
2 changes: 1 addition & 1 deletion target/nextflow/tabula_sapiens/concat/main.nf
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Expand Up @@ -156,7 +156,7 @@ thisConfig = processConfig(jsonSlurper.parseText('''{
"config" : "/home/runner/work/utilities/utilities/src/tabula_sapiens/concat/config.vsh.yaml",
"platform" : "nextflow",
"viash_version" : "0.7.3",
"git_commit" : "0120a8e813499e4a6c690a375ba663aea07fca8a",
"git_commit" : "1c80b24785f7ee036cd00534f1d36a6c9d9855b7",
"git_remote" : "https://github.com/czbiohub/utilities"
}
}'''))
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