mirror of
https://github.com/MillironX/nf-core_modules.git
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572abb00b3
* Remove def from module options definition in main
* Fix bismark_deduplicate tests
* Fix bwameth_align tests
* Fixing gatk4 conda tests ("=" instead of ':' in build id)
* Same as previous commit (Fix gatk4 test)
* Fix qualimap bamqc test (no md5 check for pngs)
* Fix seqkit split2 tests. Changed to new test data
* Fix samtools tests. Some were missing initOptions include
* Removing TOOL SUBTOOL template module since now it is included on tools repo
46 lines
1.5 KiB
Text
46 lines
1.5 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process CAT_FASTQ {
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tag "$meta.id"
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'merged_fastq', publish_id:meta.id) }
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conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img"
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} else {
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container "biocontainers/biocontainers:v1.2.0_cv1"
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}
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input:
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tuple val(meta), path(reads)
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output:
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tuple val(meta), path("*.merged.fastq.gz"), emit: reads
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def readList = reads.collect{ it.toString() }
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if (meta.single_end) {
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if (readList.size > 1) {
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"""
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cat ${readList.sort().join(' ')} > ${prefix}.merged.fastq.gz
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"""
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}
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} else {
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if (readList.size > 2) {
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def read1 = []
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def read2 = []
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readList.eachWithIndex{ v, ix -> ( ix & 1 ? read2 : read1 ) << v }
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"""
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cat ${read1.sort().join(' ')} > ${prefix}_1.merged.fastq.gz
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cat ${read2.sort().join(' ')} > ${prefix}_2.merged.fastq.gz
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"""
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}
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}
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}
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