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Update PORECHOP module to output log file (#1870)

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Update porechop to output log file
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James A. Fellows Yates 2022-07-12 16:07:31 +02:00 committed by GitHub
parent ec806cebf1
commit b78e19b9da
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3 changed files with 11 additions and 2 deletions
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4
modules/porechop/main.nf
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@ -12,6 +12,7 @@ process PORECHOP {
output: output:
tuple val(meta), path("*.fastq.gz"), emit: reads tuple val(meta), path("*.fastq.gz"), emit: reads
tuple val(meta), path("*.log") , emit: log
path "versions.yml" , emit: versions path "versions.yml" , emit: versions
when: when:
@ -25,7 +26,8 @@ process PORECHOP {
-i $reads \\ -i $reads \\
-t $task.cpus \\ -t $task.cpus \\
$args \\ $args \\
-o ${prefix}.fastq.gz -o ${prefix}.fastq.gz \\
> ${prefix}.log
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

5
modules/porechop/meta.yml
View file

@ -38,6 +38,10 @@ output:
type: file type: file
description: Demultiplexed and/or adapter-trimmed fastq.gz file description: Demultiplexed and/or adapter-trimmed fastq.gz file
pattern: "*.{fastq.gz}" pattern: "*.{fastq.gz}"
- log:
type: file
description: Log file containing stdout information
pattern: "*.log"
authors: authors:
- "@ggabernet" - "@ggabernet"
@ -48,3 +52,4 @@ authors:
- "@jonasscheid" - "@jonasscheid"
- "@jonoave" - "@jonoave"
- "@GokceOGUZ" - "@GokceOGUZ"
- "@jfy133"

4
tests/modules/porechop/test.yml
View file

@ -1,7 +1,9 @@
- name: porechop test_porechop - name: porechop test_porechop
command: nextflow run ./tests/modules/porechop -entry test_porechop -c ./tests/config/nextflow.config -c ./tests/modules/porechop/nextflow.config command: nextflow run ./tests/modules/porechop -entry test_porechop -c ./tests/config/nextflow.config -c ./tests/modules/porechop/nextflow.config
tags: tags:
- porechop - porechop
files: files:
- path: output/porechop/test_porechop.fastq.gz - path: output/porechop/test_porechop.fastq.gz
md5sum: 08f314ae9f162c8dcc27e5b513d2064d md5sum: 08f314ae9f162c8dcc27e5b513d2064d
- path: output/porechop/test_porechop.log
contains: ["Saving trimmed reads to file"]