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Update filtlong module to output log file (#1873)

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Redirect logging information to log file in filtlong module
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Sofia Stamouli 2022-07-12 17:05:31 +02:00 committed by GitHub
parent b78e19b9da
commit 957cb9b836
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3 changed files with 14 additions and 7 deletions
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4
modules/filtlong/main.nf
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@ -12,7 +12,8 @@ process FILTLONG {
output: output:
tuple val(meta), path("*.fastq.gz"), emit: reads tuple val(meta), path("*.fastq.gz"), emit: reads
path "versions.yml" , emit: versions tuple val(meta), path("*.log") , emit: log
path "versions.yml" , emit: versions
when: when:
task.ext.when == null || task.ext.when task.ext.when == null || task.ext.when
@ -27,6 +28,7 @@ process FILTLONG {
$short_reads \\ $short_reads \\
$args \\ $args \\
$longreads \\ $longreads \\
2> ${prefix}.log \\
| gzip -n > ${prefix}.fastq.gz | gzip -n > ${prefix}.fastq.gz
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml

5
modules/filtlong/meta.yml
View file

@ -45,6 +45,11 @@ output:
type: file type: file
description: Filtered (compressed) fastq file description: Filtered (compressed) fastq file
pattern: "*.fastq.gz" pattern: "*.fastq.gz"
- log:
type: file
description: Standard error logging file containing summary statistics
pattern: "*.log"
authors: authors:
- "@d4straub" - "@d4straub"
- "@sofstam"

12
tests/modules/filtlong/test.yml
View file

@ -4,8 +4,8 @@
- filtlong - filtlong
files: files:
- path: output/filtlong/test_lr.fastq.gz - path: output/filtlong/test_lr.fastq.gz
contains: - path: output/filtlong/test_lr.log
- "@00068f7a-51b3-4933-8fc6-7d6e29181ff9" contains: ["Scoring long reads"]
- name: filtlong test_filtlong_illumina_se - name: filtlong test_filtlong_illumina_se
command: nextflow run ./tests/modules/filtlong -entry test_filtlong_illumina_se -c ./tests/config/nextflow.config -c ./tests/modules/filtlong/nextflow.config command: nextflow run ./tests/modules/filtlong -entry test_filtlong_illumina_se -c ./tests/config/nextflow.config -c ./tests/modules/filtlong/nextflow.config
@ -13,8 +13,8 @@
- filtlong - filtlong
files: files:
- path: output/filtlong/test_lr.fastq.gz - path: output/filtlong/test_lr.fastq.gz
contains: - path: output/filtlong/test_lr.log
- "@00068f7a-51b3-4933-8fc6-7d6e29181ff9" contains: ["Scoring long reads"]
- name: filtlong test_filtlong_illumina_pe - name: filtlong test_filtlong_illumina_pe
command: nextflow run ./tests/modules/filtlong -entry test_filtlong_illumina_pe -c ./tests/config/nextflow.config -c ./tests/modules/filtlong/nextflow.config command: nextflow run ./tests/modules/filtlong -entry test_filtlong_illumina_pe -c ./tests/config/nextflow.config -c ./tests/modules/filtlong/nextflow.config
@ -22,5 +22,5 @@
- filtlong - filtlong
files: files:
- path: output/filtlong/test_lr.fastq.gz - path: output/filtlong/test_lr.fastq.gz
contains: - path: output/filtlong/test_lr.log
- "@00068f7a-51b3-4933-8fc6-7d6e29181ff9" contains: ["Scoring long reads"]