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Biobambam/bamsormadup: Fix name collision (#1900)

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* Fix name collision

Add stageAs to avoid name collisions

* fix version check

* fix test
This commit is contained in:
Matthias De Smet 2022-07-18 15:43:02 +02:00 committed by GitHub
parent 720027275c
commit 035e418369
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GPG key ID: 4AEE18F83AFDEB23
2 changed files with 5 additions and 6 deletions
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4
modules/biobambam/bamsormadup/main.nf
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@ -6,7 +6,7 @@ process BIOBAMBAM_BAMSORMADUP {
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/biobambam:2.0.183--h9f5acd7_1' : 'quay.io/biocontainers/biobambam:2.0.183--h9f5acd7_1'}" container "${ 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'}"
input: input:
tuple val(meta), path(bams) tuple val(meta), path(bams, stageAs: "?/*")
path(fasta) path(fasta)
output: output:
@ -39,7 +39,7 @@ process BIOBAMBAM_BAMSORMADUP {
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
bamcat: \$(echo \$(bamsormadup --version 2>&1) | sed 's/^This is biobambam2 version //; s/..biobambam2 is .*\$//' ) bamcat: \$(echo \$(bamcat --version 2>&1) | sed 's/^This is biobambam2 version //; s/..biobambam2 is .*\$//' )
bamsormadup: \$(echo \$(bamsormadup --version 2>&1) | sed 's/^This is biobambam2 version //; s/..biobambam2 is .*\$//' ) bamsormadup: \$(echo \$(bamsormadup --version 2>&1) | sed 's/^This is biobambam2 version //; s/..biobambam2 is .*\$//' )
END_VERSIONS END_VERSIONS
""" """

7
tests/modules/biobambam/bamsormadup/test.yml
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@ -1,11 +1,10 @@
- name: biobambam bamsormadup test_biobambam_bamsormadup - name: biobambam bamsormadup test_biobambam_bamsormadup
command: nextflow run tests/modules/biobambam/bamsormadup -entry test_biobambam_bamsormadup -c tests/config/nextflow.config command: nextflow run ./tests/modules/biobambam/bamsormadup -entry test_biobambam_bamsormadup -c ./tests/config/nextflow.config -c ./tests/modules/biobambam/bamsormadup/nextflow.config
tags: tags:
- biobambam/bamsormadup
- biobambam - biobambam
- biobambam/bamsormadup
files: files:
- path: output/biobambam/test.bam - path: output/biobambam/test.bam
md5sum: 243a77fb0642fd46bb16a4d3432d19dc md5sum: 1d549a00b065584c298594180ca9f3bc
- path: output/biobambam/test.metrics.txt - path: output/biobambam/test.metrics.txt
md5sum: 1721879bea1f3888ecd33b35e6ee0e72 md5sum: 1721879bea1f3888ecd33b35e6ee0e72
- path: output/biobambam/versions.yml