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Add log to output from bbmap/align (#1050)

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Daniel Lundin 2021-11-10 11:27:52 +01:00 committed by GitHub
parent 7fdeed5b79
commit 8b4bfb12bb
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2 changed files with 7 additions and 1 deletions
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4
modules/bbmap/align/main.nf
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@ -24,6 +24,7 @@ process BBMAP_ALIGN {
output: output:
tuple val(meta), path("*.bam"), emit: bam tuple val(meta), path("*.bam"), emit: bam
tuple val(meta), path("*.log"), emit: log
path "versions.yml" , emit: versions path "versions.yml" , emit: versions
script: script:
@ -51,7 +52,8 @@ process BBMAP_ALIGN {
out=${prefix}.bam \\ out=${prefix}.bam \\
$options.args \\ $options.args \\
threads=$task.cpus \\ threads=$task.cpus \\
-Xmx${task.memory.toGiga()}g -Xmx${task.memory.toGiga()}g \\
&> ${prefix}.bbmap.log
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}: ${getProcessName(task.process)}:

4
tests/modules/bbmap/align/test.yml
View file

@ -6,6 +6,7 @@
files: files:
- path: output/bbmap/test.bam - path: output/bbmap/test.bam
md5sum: e0ec7f1eec537acf146fac1cbdd868d1 md5sum: e0ec7f1eec537acf146fac1cbdd868d1
- path: output/bbmap/test.bbmap.log
- name: bbmap align paired end index ref - name: bbmap align paired end index ref
command: nextflow run ./tests/modules/bbmap/align -entry test_bbmap_align_paired_end_index_ref -c tests/config/nextflow.config command: nextflow run ./tests/modules/bbmap/align -entry test_bbmap_align_paired_end_index_ref -c tests/config/nextflow.config
@ -15,6 +16,7 @@
files: files:
- path: output/bbmap/test.bam - path: output/bbmap/test.bam
md5sum: 345a72a0d58366d75dd263b107caa460 md5sum: 345a72a0d58366d75dd263b107caa460
- path: output/bbmap/test.bbmap.log
- name: bbmap align single end index ref - name: bbmap align single end index ref
command: nextflow run ./tests/modules/bbmap/align -entry test_bbmap_align_single_end_index_ref -c tests/config/nextflow.config command: nextflow run ./tests/modules/bbmap/align -entry test_bbmap_align_single_end_index_ref -c tests/config/nextflow.config
@ -24,6 +26,7 @@
files: files:
- path: output/bbmap/test.bam - path: output/bbmap/test.bam
md5sum: 95f690636581ce9b27cf8568c715ae4d md5sum: 95f690636581ce9b27cf8568c715ae4d
- path: output/bbmap/test.bbmap.log
- name: bbmap align paired end index ref pigz - name: bbmap align paired end index ref pigz
command: nextflow run ./tests/modules/bbmap/align -entry test_bbmap_align_paired_end_index_ref_pigz -c tests/config/nextflow.config command: nextflow run ./tests/modules/bbmap/align -entry test_bbmap_align_paired_end_index_ref_pigz -c tests/config/nextflow.config
@ -33,3 +36,4 @@
files: files:
- path: output/bbmap/test.bam - path: output/bbmap/test.bam
md5sum: 441c4f196b9a82c7b224903538064308 md5sum: 441c4f196b9a82c7b224903538064308
- path: output/bbmap/test.bbmap.log