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taxprofiler/subworkflows/local/shortread_fastp.nf

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//
// Process short raw reads with FastP
//
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include { FASTP as FASTP_SINGLE } from '../../modules/nf-core/modules/fastp/main'
include { FASTP as FASTP_PAIRED } from '../../modules/nf-core/modules/fastp/main'
workflow SHORTREAD_FASTP {
take:
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reads // [[meta], [reads]]
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main:
ch_versions = Channel.empty()
ch_multiqc_files = Channel.empty()
ch_input_for_fastp = reads
.branch{
single: it[0]['single_end'] == true
paired: it[0]['single_end'] == false
}
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 )
if ( params.shortread_clipmerge_mergepairs ) {
ch_fastp_reads_prepped_pe = FASTP_PAIRED.out.reads_merged
.map {
meta, reads ->
def meta_new = meta.clone()
meta_new['single_end'] = 1
[ meta_new, reads ]
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}
ch_fastp_reads_prepped = ch_fastp_reads_prepped_pe.mix( FASTP_SINGLE.out.reads )
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} else {
ch_fastp_reads_prepped = FASTP_PAIRED.out.reads
.mix( FASTP_SINGLE.out.reads )
}
ch_versions = ch_versions.mix(FASTP_SINGLE.out.versions.first())
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 )
ch_multiqc_files = ch_multiqc_files.mix( FASTP_PAIRED.out.json )
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emit:
reads = ch_processed_reads // channel: [ val(meta), [ reads ] ]
versions = ch_versions // channel: [ versions.yml ]
mqc = ch_multiqc_files
}