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Remove unused module and fix module structure for samplesheet_check

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This commit is contained in:
James Fellows Yates 2023-03-02 13:34:10 +01:00
parent d9f687667e
commit a14937f668
2 changed files with 4 additions and 31 deletions
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31
modules/local/ensure_fastq_extension.nf
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@ -1,31 +0,0 @@
process ENSURE_FASTQ_EXTENSION {
tag "$meta.id"
label 'process_low'
conda "conda-forge::bash=5.0
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv2/biocontainers_v1.2.0_cv2.img' :
'biocontainers/biocontainers:v1.2.0_cv2' }"
input:
tuple val(meta), path(reads)
output:
tuple val(meta), path('*.fastq.gz'), emit: reads
script:
if (meta.single_end) {
fastq = "${reads.baseName}.fastq.gz"
"""
ln -s '${reads}' '${fastq}'
"""
} else {
first = "${reads[0].baseName}.fastq.gz"
second = "${reads[1].baseName}.fastq.gz"
"""
ln -s '${reads[0]}' '${first}'
ln -s '${reads[1]}' '${second}'
"""
}
}

4
modules/local/samplesheet_check.nf
View file

@ -1,5 +1,6 @@
process SAMPLESHEET_CHECK { process SAMPLESHEET_CHECK {
tag "$samplesheet" tag "$samplesheet"
label 'process_single'
conda "conda-forge::python=3.8.3" conda "conda-forge::python=3.8.3"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@ -13,6 +14,9 @@ process SAMPLESHEET_CHECK {
path '*.csv' , emit: csv path '*.csv' , emit: csv
path "versions.yml", emit: versions path "versions.yml", emit: versions
when:
task.ext.when == null || task.ext.when
script: // This script is bundled with the pipeline, in nf-core/taxprofiler/bin/ script: // This script is bundled with the pipeline, in nf-core/taxprofiler/bin/
""" """
check_samplesheet.py \\ check_samplesheet.py \\