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55 lines
2 KiB
Text
55 lines
2 KiB
Text
//
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// Process short raw reads with FastP
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//
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include { FASTP as FASTP_SINGLE } from '../../modules/nf-core/modules/fastp/main'
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include { FASTP as FASTP_PAIRED } from '../../modules/nf-core/modules/fastp/main'
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workflow SHORTREAD_FASTP {
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take:
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reads // [[meta], [reads]]
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main:
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ch_versions = Channel.empty()
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ch_multiqc_files = Channel.empty()
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ch_input_for_fastp = reads
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.branch{
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single: it[0]['single_end'] == true
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paired: it[0]['single_end'] == false
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}
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FASTP_SINGLE ( ch_input_for_fastp.single, false, false )
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// Last parameter here turns on merging of PE data
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FASTP_PAIRED ( ch_input_for_fastp.paired, false, params.shortread_clipmerge_mergepairs )
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if ( params.shortread_clipmerge_mergepairs ) {
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ch_fastp_reads_prepped_pe = FASTP_PAIRED.out.reads_merged
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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 ].flatten() ]
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}
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ch_fastp_reads_prepped = ch_fastp_reads_prepped_pe.mix( FASTP_SINGLE.out.reads )
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} else {
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ch_fastp_reads_prepped = FASTP_PAIRED.out.reads
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.mix( FASTP_SINGLE.out.reads )
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}
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ch_versions = ch_versions.mix(FASTP_SINGLE.out.versions.first())
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ch_versions = ch_versions.mix(FASTP_PAIRED.out.versions.first())
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ch_processed_reads = ch_fastp_reads_prepped
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ch_multiqc_files = ch_multiqc_files.mix( FASTP_SINGLE.out.json )
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ch_multiqc_files = ch_multiqc_files.mix( FASTP_PAIRED.out.json )
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emit:
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reads = ch_processed_reads // channel: [ val(meta), [ reads ] ]
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versions = ch_versions // channel: [ versions.yml ]
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mqc = ch_multiqc_files
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}
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