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Build branch save-params with version save-params (05ac6a3)

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Build pipeline: viash-hub.htrnaseq.save-params-h88fh

Source commit: 05ac6a3d24

Source message: updated filepathpath parsing
This commit is contained in:
CI
2025-04-01 16:03:23 +00:00
parent 8bf692c37b
commit 8ca2889a4d
86 changed files with 11389 additions and 2343 deletions
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9
target/executable/stats/combine_star_logs/.config.vsh.yaml
View File

@@ -91,6 +91,9 @@ test_resources:
path: "test_data"
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
@@ -197,8 +200,8 @@ build_info:
engine: "docker|native"
output: "target/executable/stats/combine_star_logs"
executable: "target/executable/stats/combine_star_logs/combine_star_logs"
viash_version: "0.9.0"
git_commit: "1561d769c65192a820053a565654dee8cbe55588"
viash_version: "0.9.2"
git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
@@ -208,7 +211,7 @@ package_config:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
dest: "resources_test"
viash_version: "0.9.0"
viash_version: "0.9.2"
source: "src"
target: "target"
config_mods:

98
target/executable/stats/combine_star_logs/combine_star_logs
View File

@@ -2,7 +2,7 @@
# combine_star_logs save-params
#
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
@@ -172,39 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "combine_star_logs save-params"
echo ""
echo "Arguments:"
echo " --barcodes"
echo " type: string, required parameter, multiple values allowed"
echo " Barcodes responding to the respective log files."
echo ""
echo " --star_logs"
echo " type: file, required parameter, multiple values allowed, file must exist"
echo " example: Log.final.out"
echo " Paths to the STAR log files (most frequently called Log.final.out)"
echo ""
echo " --gene_summary_logs"
echo " type: file, required parameter, multiple values allowed, file must exist"
echo " example: Summary.txt"
echo " Paths to the Summary.csv files from the STAR Solo output. Can be found"
echo " in"
echo " the 'Solo.out/Gene' folder relative to the root of the STAR output"
echo " directory."
echo ""
echo " --reads_per_gene_logs"
echo " type: file, required parameter, multiple values allowed, file must exist"
echo " Paths to the 'ReadsPerGene.out.tab' files as output by STAR."
echo ""
echo " --output"
echo " type: file, output, file must exist"
echo " default: starLogs.txt"
echo " Tab-delimited file describing for each barcode (as the rows), the"
echo " metrics (as columns)"
echo " gathered from the different input files."
}
# initialise variables
VIASH_MODE='run'
@@ -490,9 +457,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dries Schaumont"
LABEL org.opencontainers.image.description="Companion container for running component stats combine_star_logs"
LABEL org.opencontainers.image.created="2025-03-25T15:33:56Z"
LABEL org.opencontainers.image.created="2025-04-01T15:16:01Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="1561d769c65192a820053a565654dee8cbe55588"
LABEL org.opencontainers.image.revision="05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
LABEL org.opencontainers.image.version="save-params"
VIASHDOCKER
@@ -607,6 +574,65 @@ fi
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "combine_star_logs save-params"
echo ""
echo "Arguments:"
echo " --barcodes"
echo " type: string, required parameter, multiple values allowed"
echo " Barcodes responding to the respective log files."
echo ""
echo " --star_logs"
echo " type: file, required parameter, multiple values allowed, file must exist"
echo " example: Log.final.out"
echo " Paths to the STAR log files (most frequently called Log.final.out)"
echo ""
echo " --gene_summary_logs"
echo " type: file, required parameter, multiple values allowed, file must exist"
echo " example: Summary.txt"
echo " Paths to the Summary.csv files from the STAR Solo output. Can be found"
echo " in"
echo " the 'Solo.out/Gene' folder relative to the root of the STAR output"
echo " directory."
echo ""
echo " --reads_per_gene_logs"
echo " type: file, required parameter, multiple values allowed, file must exist"
echo " Paths to the 'ReadsPerGene.out.tab' files as output by STAR."
echo ""
echo " --output"
echo " type: file, output, file must exist"
echo " default: starLogs.txt"
echo " Tab-delimited file describing for each barcode (as the rows), the"
echo " metrics (as columns)"
echo " gathered from the different input files."
echo ""
echo "Viash built in Computational Requirements:"
echo " ---cpus=INT"
echo " Number of CPUs to use"
echo " ---memory=STRING"
echo " Amount of memory to use. Examples: 4GB, 3MiB."
echo ""
echo "Viash built in Docker:"
echo " ---setup=STRATEGY"
echo " Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
echo " Default: ifneedbepullelsecachedbuild"
echo " ---dockerfile"
echo " Print the dockerfile to stdout."
echo " ---docker_run_args=ARG"
echo " Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
echo " ---docker_image_id"
echo " Print the docker image id to stdout."
echo " ---debug"
echo " Enter the docker container for debugging purposes."
echo ""
echo "Viash built in Engines:"
echo " ---engine=ENGINE_ID"
echo " Specify the engine to use. Options are: docker, native."
echo " Default: docker"
}
# initialise array
VIASH_POSITIONAL_ARGS=''

9
target/executable/stats/generate_pool_statistics/.config.vsh.yaml
View File

@@ -75,6 +75,9 @@ test_resources:
is_executable: true
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
@@ -181,8 +184,8 @@ build_info:
engine: "docker|native"
output: "target/executable/stats/generate_pool_statistics"
executable: "target/executable/stats/generate_pool_statistics/generate_pool_statistics"
viash_version: "0.9.0"
git_commit: "1561d769c65192a820053a565654dee8cbe55588"
viash_version: "0.9.2"
git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
@@ -192,7 +195,7 @@ package_config:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
dest: "resources_test"
viash_version: "0.9.0"
viash_version: "0.9.2"
source: "src"
target: "target"
config_mods:

82
target/executable/stats/generate_pool_statistics/generate_pool_statistics
View File

@@ -2,7 +2,7 @@
# generate_pool_statistics save-params
#
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
@@ -173,31 +173,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "generate_pool_statistics save-params"
echo ""
echo "Arguments:"
echo " --nrReadsNrGenesPerChrom"
echo " type: file, multiple values allowed, file must exist"
echo " default: processedBamFile_well1.tsv;processedBamfile_well2.tsv"
echo " Path to an output file that contains a .tsv formatted table describing"
echo " per chromosome the number of reads that were mapped to that chromosome"
echo " (NumberOfReads"
echo " column) and the number of genes on that chromosome that had at least one"
echo " read mapped to it (NumberOfGenes)."
echo ""
echo " --nrReadsNrGenesPerChromPool"
echo " type: file, output, file must exist"
echo " example: nrReadsNrGenesPerChrom.txt"
echo " Pivot table in tsv format of the combined input nrReadsNrGenesPerChrom"
echo " files. Describes"
echo " per chromosome (as columns) the number of reads, as well as the total"
echo " number"
echo " of reads per cell barcode and the percentage of nuclear, ERCC and"
echo " mitochondrial"
echo " reads."
}
# initialise variables
VIASH_MODE='run'
@@ -483,9 +458,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
LABEL org.opencontainers.image.description="Companion container for running component stats generate_pool_statistics"
LABEL org.opencontainers.image.created="2025-03-25T15:33:56Z"
LABEL org.opencontainers.image.created="2025-04-01T15:16:02Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="1561d769c65192a820053a565654dee8cbe55588"
LABEL org.opencontainers.image.revision="05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
LABEL org.opencontainers.image.version="save-params"
VIASHDOCKER
@@ -600,6 +575,57 @@ fi
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "generate_pool_statistics save-params"
echo ""
echo "Arguments:"
echo " --nrReadsNrGenesPerChrom"
echo " type: file, multiple values allowed, file must exist"
echo " default: processedBamFile_well1.tsv;processedBamfile_well2.tsv"
echo " Path to an output file that contains a .tsv formatted table describing"
echo " per chromosome the number of reads that were mapped to that chromosome"
echo " (NumberOfReads"
echo " column) and the number of genes on that chromosome that had at least one"
echo " read mapped to it (NumberOfGenes)."
echo ""
echo " --nrReadsNrGenesPerChromPool"
echo " type: file, output, file must exist"
echo " example: nrReadsNrGenesPerChrom.txt"
echo " Pivot table in tsv format of the combined input nrReadsNrGenesPerChrom"
echo " files. Describes"
echo " per chromosome (as columns) the number of reads, as well as the total"
echo " number"
echo " of reads per cell barcode and the percentage of nuclear, ERCC and"
echo " mitochondrial"
echo " reads."
echo ""
echo "Viash built in Computational Requirements:"
echo " ---cpus=INT"
echo " Number of CPUs to use"
echo " ---memory=STRING"
echo " Amount of memory to use. Examples: 4GB, 3MiB."
echo ""
echo "Viash built in Docker:"
echo " ---setup=STRATEGY"
echo " Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
echo " Default: ifneedbepullelsecachedbuild"
echo " ---dockerfile"
echo " Print the dockerfile to stdout."
echo " ---docker_run_args=ARG"
echo " Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
echo " ---docker_image_id"
echo " Print the docker image id to stdout."
echo " ---debug"
echo " Enter the docker container for debugging purposes."
echo ""
echo "Viash built in Engines:"
echo " ---engine=ENGINE_ID"
echo " Specify the engine to use. Options are: docker, native."
echo " Default: docker"
}
# initialise array
VIASH_POSITIONAL_ARGS=''

9
target/executable/stats/generate_well_statistics/.config.vsh.yaml
View File

@@ -146,6 +146,9 @@ test_resources:
path: "empty.sam"
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
@@ -263,8 +266,8 @@ build_info:
engine: "docker|native"
output: "target/executable/stats/generate_well_statistics"
executable: "target/executable/stats/generate_well_statistics/generate_well_statistics"
viash_version: "0.9.0"
git_commit: "1561d769c65192a820053a565654dee8cbe55588"
viash_version: "0.9.2"
git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
@@ -274,7 +277,7 @@ package_config:
test_resources:
- path: "gs://viash-hub-test-data/htrnaseq/v1/"
dest: "resources_test"
viash_version: "0.9.0"
viash_version: "0.9.2"
source: "src"
target: "target"
config_mods:

150
target/executable/stats/generate_well_statistics/generate_well_statistics
View File

@@ -2,7 +2,7 @@
# generate_well_statistics save-params
#
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
@@ -173,65 +173,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "generate_well_statistics save-params"
echo ""
echo "Generate summary statistics from BAM files generated by STAR solo."
echo ""
echo "Arguments:"
echo " --input"
echo " type: file, file must exist"
echo " example: input.bam"
echo " The .bam file as returned by the mapping tool STAR."
echo ""
echo " --barcode"
echo " type: string, required parameter"
echo " The barcode for the well that is being processed. Is only used to add a"
echo " metadata"
echo " column to all output files."
echo ""
echo " --well_id"
echo " type: string, required parameter"
echo " ID of this well. Only used to add a metadata column to the output files."
echo ""
echo " --processedBAMFile"
echo " type: file, output, file must exist"
echo " default: processedBamFile.txt"
echo " Path to a .tsv file listing, per read in the BAM file,"
echo " the value for the \"CB\", \"UX\", \"GX\" and \"GN\" tag, together with the"
echo " chromsome to which the read was mapped to."
echo ""
echo " --nrReadsNrGenesPerChrom"
echo " type: file, output, file must exist"
echo " default: nrReadsNrGenesPerChrom.txt"
echo " Path to an output file that contains a .tsv formatted table describing"
echo " per chromosome the number of reads that were mapped to that chromosome"
echo " (NumberOfReads"
echo " column) and the number of genes on that chromosome that had at least one"
echo " read mapped to it (NumberOfGenes)."
echo ""
echo " --nrReadsNrUMIsPerCB"
echo " type: file, output, file must exist"
echo " default: nrReadsNrUMIsPerCB.txt"
echo " Path to an output file that contains a .tsv formatted table describing"
echo " per barcode the number of UMI's (nrUMIs) and the total number of reads"
echo " (NumberOfReads)."
echo ""
echo " --umiFreqTop"
echo " type: file, output, file must exist"
echo " default: umiFreqTop100.txt"
echo " Path to an output file that contains a .tsv formatted table describing"
echo " per UMI (column UB) the frequency at which they occur in the reads"
echo " (column"
echo " N). Only the top 100 UMIs are included."
echo ""
echo " --threads"
echo " type: integer"
echo " default: 1"
echo " min: 1"
echo " Number of threads to use for decompressing BAM files."
}
# initialise variables
VIASH_MODE='run'
@@ -520,9 +461,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
LABEL org.opencontainers.image.description="Companion container for running component stats generate_well_statistics"
LABEL org.opencontainers.image.created="2025-03-25T15:33:56Z"
LABEL org.opencontainers.image.created="2025-04-01T15:16:01Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="1561d769c65192a820053a565654dee8cbe55588"
LABEL org.opencontainers.image.revision="05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
LABEL org.opencontainers.image.version="save-params"
VIASHDOCKER
@@ -637,6 +578,91 @@ fi
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "generate_well_statistics save-params"
echo ""
echo "Generate summary statistics from BAM files generated by STAR solo."
echo ""
echo "Arguments:"
echo " --input"
echo " type: file, file must exist"
echo " example: input.bam"
echo " The .bam file as returned by the mapping tool STAR."
echo ""
echo " --barcode"
echo " type: string, required parameter"
echo " The barcode for the well that is being processed. Is only used to add a"
echo " metadata"
echo " column to all output files."
echo ""
echo " --well_id"
echo " type: string, required parameter"
echo " ID of this well. Only used to add a metadata column to the output files."
echo ""
echo " --processedBAMFile"
echo " type: file, output, file must exist"
echo " default: processedBamFile.txt"
echo " Path to a .tsv file listing, per read in the BAM file,"
echo " the value for the \"CB\", \"UX\", \"GX\" and \"GN\" tag, together with the"
echo " chromsome to which the read was mapped to."
echo ""
echo " --nrReadsNrGenesPerChrom"
echo " type: file, output, file must exist"
echo " default: nrReadsNrGenesPerChrom.txt"
echo " Path to an output file that contains a .tsv formatted table describing"
echo " per chromosome the number of reads that were mapped to that chromosome"
echo " (NumberOfReads"
echo " column) and the number of genes on that chromosome that had at least one"
echo " read mapped to it (NumberOfGenes)."
echo ""
echo " --nrReadsNrUMIsPerCB"
echo " type: file, output, file must exist"
echo " default: nrReadsNrUMIsPerCB.txt"
echo " Path to an output file that contains a .tsv formatted table describing"
echo " per barcode the number of UMI's (nrUMIs) and the total number of reads"
echo " (NumberOfReads)."
echo ""
echo " --umiFreqTop"
echo " type: file, output, file must exist"
echo " default: umiFreqTop100.txt"
echo " Path to an output file that contains a .tsv formatted table describing"
echo " per UMI (column UB) the frequency at which they occur in the reads"
echo " (column"
echo " N). Only the top 100 UMIs are included."
echo ""
echo " --threads"
echo " type: integer"
echo " default: 1"
echo " min: 1"
echo " Number of threads to use for decompressing BAM files."
echo ""
echo "Viash built in Computational Requirements:"
echo " ---cpus=INT"
echo " Number of CPUs to use"
echo " ---memory=STRING"
echo " Amount of memory to use. Examples: 4GB, 3MiB."
echo ""
echo "Viash built in Docker:"
echo " ---setup=STRATEGY"
echo " Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
echo " Default: ifneedbepullelsecachedbuild"
echo " ---dockerfile"
echo " Print the dockerfile to stdout."
echo " ---docker_run_args=ARG"
echo " Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
echo " ---docker_image_id"
echo " Print the docker image id to stdout."
echo " ---debug"
echo " Enter the docker container for debugging purposes."
echo ""
echo "Viash built in Engines:"
echo " ---engine=ENGINE_ID"
echo " Specify the engine to use. Options are: docker, native."
echo " Default: docker"
}
# initialise array
VIASH_POSITIONAL_ARGS=''