Corrected pytest and config

This commit is contained in:
sruthipsuresh 2021-01-08 13:44:02 -06:00
parent a108bd407e
commit 70de0331a5
12 changed files with 13 additions and 13 deletions

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@ -37,4 +37,4 @@ jobs:
run: python -m pip install --upgrade pip pytest-workflow run: python -m pip install --upgrade pip pytest-workflow
# Test the module # Test the module
- run: pytest --tag bedtools_merge--symlink --wt 2 - run: pytest --tag bedtools_merge --symlink --wt 2

View file

@ -37,4 +37,4 @@ jobs:
run: python -m pip install --upgrade pip pytest-workflow run: python -m pip install --upgrade pip pytest-workflow
# Test the module # Test the module
- run: pytest --tag bedtools_slop--symlink --wt 2 - run: pytest --tag bedtools_slop --symlink --wt 2

View file

@ -37,4 +37,4 @@ jobs:
run: python -m pip install --upgrade pip pytest-workflow run: python -m pip install --upgrade pip pytest-workflow
# Test the module # Test the module
- run: pytest --tag bedtools_sort--symlink --wt 2 - run: pytest --tag bedtools_sort --symlink --wt 2

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@ -56,4 +56,4 @@ def saveFiles(Map args) {
return "${getPathFromList(path_list)}/$args.filename" return "${getPathFromList(path_list)}/$args.filename"
} }
} }
} }

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@ -16,7 +16,7 @@ process BEDTOOLS_COMPLEMENT {
} else { } else {
container "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0" container "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0"
} }
input: input:
tuple val(meta), path(beds), path (sizes) tuple val(meta), path(beds), path (sizes)

View file

@ -56,4 +56,4 @@ def saveFiles(Map args) {
return "${getPathFromList(path_list)}/$args.filename" return "${getPathFromList(path_list)}/$args.filename"
} }
} }
} }

View file

@ -56,4 +56,4 @@ def saveFiles(Map args) {
return "${getPathFromList(path_list)}/$args.filename" return "${getPathFromList(path_list)}/$args.filename"
} }
} }
} }

View file

@ -9,7 +9,7 @@ process BEDTOOLS_INTERSECT {
publishDir "${params.outdir}", publishDir "${params.outdir}",
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::bedtools =2.29.2" : null) conda (params.enable_conda ? "bioconda::bedtools =2.29.2" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bedtools:2.29.2--hc088bd4_0" container "https://depot.galaxyproject.org/singularity/bedtools:2.29.2--hc088bd4_0"

View file

@ -56,4 +56,4 @@ def saveFiles(Map args) {
return "${getPathFromList(path_list)}/$args.filename" return "${getPathFromList(path_list)}/$args.filename"
} }
} }
} }

View file

@ -56,4 +56,4 @@ def saveFiles(Map args) {
return "${getPathFromList(path_list)}/$args.filename" return "${getPathFromList(path_list)}/$args.filename"
} }
} }
} }

View file

@ -16,7 +16,7 @@ process BEDTOOLS_SLOP {
} else { } else {
container "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0" container "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0"
} }
input: input:
tuple val(meta), path(beds), path (sizes) tuple val(meta), path(beds), path (sizes)
@ -42,6 +42,6 @@ process BEDTOOLS_SLOP {
""" """
slopBed -i $beds -g $sizes -l $params.l -r $params.r $header $pct $options.args> ${prefix}.slop.bed slopBed -i $beds -g $sizes -l $params.l -r $params.r $header $pct $options.args> ${prefix}.slop.bed
bedtools --version | sed -e "s/Bedtools v//g" > ${software}.version.txt bedtools --version | sed -e "s/Bedtools v//g" > ${software}.version.txt
""" """
} }
} }

View file

@ -56,4 +56,4 @@ def saveFiles(Map args) {
return "${getPathFromList(path_list)}/$args.filename" return "${getPathFromList(path_list)}/$args.filename"
} }
} }
} }