mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-10 23:23:09 +00:00
fix: insert .fastq
file extension
The MetaPhlAn3 module computes the input type from the file extension without the possibility to configure an override. Since AdapterRemoval2 creates files without `.fastq` extensions, MetaPhlAn3 input was determined to be SAM.
This commit is contained in:
parent
4eab257d68
commit
be93eae640
2 changed files with 118 additions and 39 deletions
31
modules/local/ensure_fastq_extension.nf
Normal file
31
modules/local/ensure_fastq_extension.nf
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@ -0,0 +1,31 @@
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process ENSURE_FASTQ_EXTENSION {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "conda-forge::bash=5.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv2/biocontainers_v1.2.0_cv2.img' :
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'biocontainers/biocontainers:v1.2.0_cv2' }"
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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('*.fastq.gz'), emit: reads
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script:
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if (meta.single_end) {
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fastq = "${reads.baseName}.fastq.gz"
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"""
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ln -s '${reads}' '${fastq}'
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"""
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} else {
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first = "${reads[0].baseName}.fastq.gz"
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second = "${reads[1].baseName}.fastq.gz"
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"""
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ln -s '${reads[0]}' '${first}'
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ln -s '${reads[1]}' '${second}'
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"""
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}
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}
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@ -5,6 +5,11 @@ Process short raw reads with AdapterRemoval
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include { ADAPTERREMOVAL as ADAPTERREMOVAL_SINGLE } from '../../modules/nf-core/modules/adapterremoval/main'
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include { ADAPTERREMOVAL as ADAPTERREMOVAL_SINGLE } from '../../modules/nf-core/modules/adapterremoval/main'
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include { ADAPTERREMOVAL as ADAPTERREMOVAL_PAIRED } from '../../modules/nf-core/modules/adapterremoval/main'
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include { ADAPTERREMOVAL as ADAPTERREMOVAL_PAIRED } from '../../modules/nf-core/modules/adapterremoval/main'
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include { CAT_FASTQ } from '../../modules/nf-core/modules/cat/fastq/main'
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include { CAT_FASTQ } from '../../modules/nf-core/modules/cat/fastq/main'
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include {
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ENSURE_FASTQ_EXTENSION as ENSURE_FASTQ_EXTENSION1;
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ENSURE_FASTQ_EXTENSION as ENSURE_FASTQ_EXTENSION2;
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ENSURE_FASTQ_EXTENSION as ENSURE_FASTQ_EXTENSION3;
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} from '../../modules/local/ensure_fastq_extension'
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workflow SHORTREAD_ADAPTERREMOVAL {
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workflow SHORTREAD_ADAPTERREMOVAL {
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@ -30,59 +35,102 @@ workflow SHORTREAD_ADAPTERREMOVAL {
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*/
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*/
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if ( params.shortread_clipmerge_mergepairs && !params.shortread_clipmerge_excludeunmerged ) {
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if ( params.shortread_clipmerge_mergepairs && !params.shortread_clipmerge_excludeunmerged ) {
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ch_adapterremoval_for_cat = ADAPTERREMOVAL_PAIRED.out.collapsed
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.mix(
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ENSURE_FASTQ_EXTENSION1(
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Channel.empty().mix(
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ADAPTERREMOVAL_PAIRED.out.collapsed,
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ADAPTERREMOVAL_PAIRED.out.collapsed_truncated,
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ADAPTERREMOVAL_PAIRED.out.collapsed_truncated,
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ADAPTERREMOVAL_PAIRED.out.singles_truncated,
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ADAPTERREMOVAL_PAIRED.out.singles_truncated,
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ADAPTERREMOVAL_PAIRED.out.pair1_truncated,
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ADAPTERREMOVAL_PAIRED.out.pair1_truncated,
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ADAPTERREMOVAL_PAIRED.out.pair2_truncated
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ADAPTERREMOVAL_PAIRED.out.pair2_truncated
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)
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)
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.map {
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.map { meta, reads ->
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meta, reads ->
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meta.single_end = true
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def meta_new = meta.clone()
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[meta, reads]
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meta_new.single_end = true
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[ meta_new, reads ]
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}
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}
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.groupTuple()
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)
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ch_adapterremoval_reads_prepped = CAT_FASTQ ( ch_adapterremoval_for_cat ).reads
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CAT_FASTQ(
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.mix( ADAPTERREMOVAL_SINGLE.out.singles_truncated )
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ENSURE_FASTQ_EXTENSION1.out.reads
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.groupTuple()
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)
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ENSURE_FASTQ_EXTENSION2(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
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ch_adapterremoval_reads_prepped = CAT_FASTQ.out.reads
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.mix(ENSURE_FASTQ_EXTENSION2.out.reads)
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} else if ( params.shortread_clipmerge_mergepairs && params.shortread_clipmerge_excludeunmerged ) {
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} else if ( params.shortread_clipmerge_mergepairs && params.shortread_clipmerge_excludeunmerged ) {
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ch_adapterremoval_for_cat = ADAPTERREMOVAL_PAIRED.out.collapsed
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.mix( ADAPTERREMOVAL_PAIRED.out.collapsed_truncated )
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.map {
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meta, reads ->
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def meta_new = meta.clone()
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meta_new['single_end'] = true
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[ meta_new, reads ]
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ENSURE_FASTQ_EXTENSION1(
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Channel.empty().mix(
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ADAPTERREMOVAL_PAIRED.out.collapsed,
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ADAPTERREMOVAL_PAIRED.out.collapsed_truncated
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)
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.map { meta, reads ->
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meta.single_end = true
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[meta, reads]
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}
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}
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.groupTuple(by: 0)
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)
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ch_adapterremoval_reads_prepped = CAT_FASTQ ( ch_adapterremoval_for_cat ).reads
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CAT_FASTQ(
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.mix( ADAPTERREMOVAL_SINGLE.out.singles_truncated )
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ENSURE_FASTQ_EXTENSION1.out.reads
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.groupTuple()
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)
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ENSURE_FASTQ_EXTENSION2(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
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ch_adapterremoval_reads_prepped = CAT_FASTQ.out.reads
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.mix(ENSURE_FASTQ_EXTENSION2.out.reads)
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} else {
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} else {
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ch_adapterremoval_reads_prepped = ADAPTERREMOVAL_PAIRED.out.pair1_truncated
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ENSURE_FASTQ_EXTENSION1(
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.join( ADAPTERREMOVAL_PAIRED.out.pair2_truncated )
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ADAPTERREMOVAL_PAIRED.out.pair1_truncated
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.map { meta, reads ->
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meta.single_end = true
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[meta, reads]
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}
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)
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ENSURE_FASTQ_EXTENSION2(
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ADAPTERREMOVAL_PAIRED.out.pair2_truncated
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.map { meta, reads ->
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meta.single_end = true
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[meta, reads]
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}
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)
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ENSURE_FASTQ_EXTENSION3(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
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ch_adapterremoval_reads_prepped = ENSURE_FASTQ_EXTENSION1.out.reads
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.join(ENSURE_FASTQ_EXTENSION2.out.reads)
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.groupTuple()
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.groupTuple()
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.map { meta, pair1, pair2 ->
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.map { meta, pair1, pair2 ->
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meta.single_end = false
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[ meta, [ pair1, pair2 ].flatten() ]
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[ meta, [ pair1, pair2 ].flatten() ]
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}
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}
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.mix( ADAPTERREMOVAL_SINGLE.out.singles_truncated )
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.mix(ENSURE_FASTQ_EXTENSION3.out.reads)
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}
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ch_processed_reads = ch_adapterremoval_reads_prepped
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}
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ch_versions = ch_versions.mix( ADAPTERREMOVAL_SINGLE.out.versions.first() )
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ch_versions = ch_versions.mix( ADAPTERREMOVAL_SINGLE.out.versions.first() )
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ch_versions = ch_versions.mix( ADAPTERREMOVAL_PAIRED.out.versions.first() )
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ch_versions = ch_versions.mix( ADAPTERREMOVAL_PAIRED.out.versions.first() )
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ch_multiqc_files = ch_multiqc_files.mix( ADAPTERREMOVAL_PAIRED.out.log.collect{it[1]}, ADAPTERREMOVAL_SINGLE.out.log.collect{it[1]} )
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ch_multiqc_files = ch_multiqc_files.mix(
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ADAPTERREMOVAL_PAIRED.out.log.collect{it[1]},
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ADAPTERREMOVAL_SINGLE.out.log.collect{it[1]}
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)
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emit:
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emit:
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reads = ch_processed_reads // channel: [ val(meta), [ reads ] ]
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reads = ch_adapterremoval_reads_prepped // channel: [ val(meta), [ reads ] ]
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versions = ch_versions // channel: [ versions.yml ]
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versions = ch_versions // channel: [ versions.yml ]
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mqc = ch_multiqc_files
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mqc = ch_multiqc_files
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}
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}
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def ensureFastQExtension(row) {
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def (meta, read) = row
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def filename = file(read.parent).resolve("${read.baseName}.fastq.gz")
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read.renameTo(filename.toString())
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return [meta, read]
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}
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