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Biobambam/bamsormadup: Fix name collision (#1900)
* Fix name collision Add stageAs to avoid name collisions * fix version check * fix test
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720027275c
commit
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2 changed files with 5 additions and 6 deletions
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@ -6,7 +6,7 @@ process BIOBAMBAM_BAMSORMADUP {
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/biobambam:2.0.183--h9f5acd7_1' : 'quay.io/biocontainers/biobambam:2.0.183--h9f5acd7_1'}"
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input:
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tuple val(meta), path(bams)
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tuple val(meta), path(bams, stageAs: "?/*")
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path(fasta)
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output:
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@ -39,7 +39,7 @@ process BIOBAMBAM_BAMSORMADUP {
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bamcat: \$(echo \$(bamsormadup --version 2>&1) | sed 's/^This is biobambam2 version //; s/..biobambam2 is .*\$//' )
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bamcat: \$(echo \$(bamcat --version 2>&1) | sed 's/^This is biobambam2 version //; s/..biobambam2 is .*\$//' )
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bamsormadup: \$(echo \$(bamsormadup --version 2>&1) | sed 's/^This is biobambam2 version //; s/..biobambam2 is .*\$//' )
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END_VERSIONS
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"""
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@ -1,11 +1,10 @@
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- name: biobambam bamsormadup test_biobambam_bamsormadup
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command: nextflow run tests/modules/biobambam/bamsormadup -entry test_biobambam_bamsormadup -c tests/config/nextflow.config
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command: nextflow run ./tests/modules/biobambam/bamsormadup -entry test_biobambam_bamsormadup -c ./tests/config/nextflow.config -c ./tests/modules/biobambam/bamsormadup/nextflow.config
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tags:
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- biobambam/bamsormadup
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- biobambam
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- biobambam/bamsormadup
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files:
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- path: output/biobambam/test.bam
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md5sum: 243a77fb0642fd46bb16a4d3432d19dc
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md5sum: 1d549a00b065584c298594180ca9f3bc
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- path: output/biobambam/test.metrics.txt
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md5sum: 1721879bea1f3888ecd33b35e6ee0e72
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- path: output/biobambam/versions.yml
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