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add stub for picard/collectwgsmtrics (#1945)

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* add stub for picard/collectwgsmtrics

* fix conda build needs to be >2.0 error and typo
This commit is contained in:
Annick Renevey 2022-08-09 09:33:15 +02:00 committed by GitHub
parent 479e0638d1
commit ac1c6ad710
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2 changed files with 20 additions and 1 deletions
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13
modules/picard/collectwgsmetrics/main.nf
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@ -2,7 +2,7 @@ process PICARD_COLLECTWGSMETRICS {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) conda (params.enable_conda ? "bioconda::picard=2.27.4 r::r-base" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }" 'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }"
@ -37,6 +37,17 @@ process PICARD_COLLECTWGSMETRICS {
--REFERENCE_SEQUENCE ${fasta} --REFERENCE_SEQUENCE ${fasta}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
picard: \$(picard CollectWgsMetrics --version 2>&1 | grep -o 'Version.*' | cut -f2- -d:)
END_VERSIONS
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.CollectWgsMetrics.coverage_metrics
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
picard: \$(picard CollectWgsMetrics --version 2>&1 | grep -o 'Version.*' | cut -f2- -d:) picard: \$(picard CollectWgsMetrics --version 2>&1 | grep -o 'Version.*' | cut -f2- -d:)

8
tests/modules/picard/collectwgsmetrics/test.yml
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@ -5,3 +5,11 @@
- picard - picard
files: files:
- path: output/picard/test.CollectWgsMetrics.coverage_metrics - path: output/picard/test.CollectWgsMetrics.coverage_metrics
- name: picard collectwgsmetrics test_picard_collectwgsmetrics stub
command: nextflow run ./tests/modules/picard/collectwgsmetrics -entry test_picard_collectwgsmetrics -c ./tests/config/nextflow.config -c ./tests/modules/picard/collectwgsmetrics/nextflow.config -stub-run
tags:
- picard/collectwgsmetrics
- picard
files:
- path: output/picard/test.CollectWgsMetrics.coverage_metrics