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refactor: remove superfluous ENSURE_FASTQ_EXTENSION
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commit
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1 changed files with 16 additions and 59 deletions
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@ -5,11 +5,6 @@ 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_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 {
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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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@ -36,34 +31,25 @@ workflow SHORTREAD_ADAPTERREMOVAL {
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if ( params.shortread_clipmerge_mergepairs && !params.shortread_clipmerge_excludeunmerged ) {
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ENSURE_FASTQ_EXTENSION1(
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Channel.empty().mix(
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ch_concat_fastq = Channel.empty()
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.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.singles_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.paired_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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CAT_FASTQ(
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ENSURE_FASTQ_EXTENSION1.out.reads
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.groupTuple()
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)
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.map { [it.head(), it.tail().flatten()] }
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ENSURE_FASTQ_EXTENSION2(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
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CAT_FASTQ(ch_concat_fastq)
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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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.mix(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
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} else if ( params.shortread_clipmerge_mergepairs && params.shortread_clipmerge_excludeunmerged ) {
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ENSURE_FASTQ_EXTENSION1(
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Channel.empty().mix(
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ch_concat_fastq = Channel.empty()
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.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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@ -71,54 +57,25 @@ workflow SHORTREAD_ADAPTERREMOVAL {
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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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CAT_FASTQ(
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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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CAT_FASTQ(ch_concat_fastq)
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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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.mix(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
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} else {
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ENSURE_FASTQ_EXTENSION1(
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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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.map { meta, pair1, pair2 ->
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meta.single_end = false
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[ meta, [ pair1, pair2 ].flatten() ]
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}
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.mix(ENSURE_FASTQ_EXTENSION3.out.reads)
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ch_adapterremoval_reads_prepped = ADAPTERREMOVAL_PAIRED.out.paired_truncated
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.mix(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
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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_PAIRED.out.versions.first() )
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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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ADAPTERREMOVAL_PAIRED.out.settings.collect{it[1]},
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ADAPTERREMOVAL_SINGLE.out.settings.collect{it[1]}
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)
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emit:
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