millironx/nf-core_modules
1
0
Fork 0
mirror of https://github.com/MillironX/nf-core_modules.git synced 2024-11-13 05:13:09 +00:00
Code Issues Releases Packages Activity

Update PORECHOP module to output log file (#1870)

Browse source 
Update porechop to output log file
This commit is contained in:
James A. Fellows Yates 2022-07-12 16:07:31 +02:00 committed by GitHub
parent ec806cebf1
commit b78e19b9da
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
3 changed files with 11 additions and 2 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

4
modules/porechop/main.nf
View file

@ -12,6 +12,7 @@ process PORECHOP {
output:
tuple val(meta), path("*.fastq.gz"), emit: reads
tuple val(meta), path("*.log") , emit: log
path "versions.yml" , emit: versions
when:
@ -25,7 +26,8 @@ process PORECHOP {
-i $reads \\
-t $task.cpus \\
$args \\
-o ${prefix}.fastq.gz
-o ${prefix}.fastq.gz \\
> ${prefix}.log
cat <<-END_VERSIONS > versions.yml
"${task.process}":

5
modules/porechop/meta.yml
View file

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

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

@ -1,7 +1,9 @@
- 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:
- porechop
files:
- path: output/porechop/test_porechop.fastq.gz
md5sum: 08f314ae9f162c8dcc27e5b513d2064d
- path: output/porechop/test_porechop.log
contains: ["Saving trimmed reads to file"]