diff --git a/modules/picard/collectwgsmetrics/main.nf b/modules/picard/collectwgsmetrics/main.nf index d3153eed..2b0aeefe 100644 --- a/modules/picard/collectwgsmetrics/main.nf +++ b/modules/picard/collectwgsmetrics/main.nf @@ -2,7 +2,7 @@ process PICARD_COLLECTWGSMETRICS { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::picard=2.27.4" : null) + conda (params.enable_conda ? "bioconda::picard=2.27.4 r::r-base" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : 'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }" @@ -37,6 +37,17 @@ process PICARD_COLLECTWGSMETRICS { --REFERENCE_SEQUENCE ${fasta} + cat <<-END_VERSIONS > versions.yml + "${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 ${prefix}.CollectWgsMetrics.coverage_metrics + cat <<-END_VERSIONS > versions.yml "${task.process}": picard: \$(picard CollectWgsMetrics --version 2>&1 | grep -o 'Version.*' | cut -f2- -d:) diff --git a/tests/modules/picard/collectwgsmetrics/test.yml b/tests/modules/picard/collectwgsmetrics/test.yml index 6e99a04c..9abba015 100644 --- a/tests/modules/picard/collectwgsmetrics/test.yml +++ b/tests/modules/picard/collectwgsmetrics/test.yml @@ -5,3 +5,11 @@ - picard files: - 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