nf-core_modules/modules/cat/fastq/main.nf
Matthieu Muffato e9bc33485e
bugfix: when there is a single input file, stageAs("?/*) returns the path directly, not in a list (#2114)
* bugfix: when there is a single input file, stageAs("?/*) returns the path directly, not in a list

* Added a test

* Added a test

* Added MD5 checksum

Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
2022-09-28 13:28:52 +01:00

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2.5 KiB
Text

process CAT_FASTQ {
tag "$meta.id"
label 'process_single'
conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'ubuntu:20.04' }"
input:
tuple val(meta), path(reads, stageAs: "input*/*")
output:
tuple val(meta), path("*.merged.fastq.gz"), emit: reads
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def readList = reads instanceof List ? reads.collect{ it.toString() } : [reads.toString()]
if (meta.single_end) {
if (readList.size >= 1) {
"""
cat ${readList.join(' ')} > ${prefix}.merged.fastq.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
END_VERSIONS
"""
}
} else {
if (readList.size >= 2) {
def read1 = []
def read2 = []
readList.eachWithIndex{ v, ix -> ( ix & 1 ? read2 : read1 ) << v }
"""
cat ${read1.join(' ')} > ${prefix}_1.merged.fastq.gz
cat ${read2.join(' ')} > ${prefix}_2.merged.fastq.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
END_VERSIONS
"""
}
}
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
def readList = reads instanceof List ? reads.collect{ it.toString() } : [reads.toString()]
if (meta.single_end) {
if (readList.size > 1) {
"""
touch ${prefix}.merged.fastq.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
END_VERSIONS
"""
}
} else {
if (readList.size > 2) {
"""
touch ${prefix}_1.merged.fastq.gz
touch ${prefix}_2.merged.fastq.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
END_VERSIONS
"""
}
}
}