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73 lines
2.6 KiB
Text
73 lines
2.6 KiB
Text
//
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// Check input samplesheet and get read channels
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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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include { FASTQC as FASTQC_POST } from '../../modules/nf-core/modules/fastqc/main'
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workflow SHORTREAD_PREPROCESSING {
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take:
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reads // file: /path/to/samplesheet.csv
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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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//
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// STEP: Read clipping and merging
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//
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// TODO give option to clip only and retain pairs
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// TODO give option to retain singletons (probably fastp option likely)
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// TODO move to subworkflow
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if ( params.shortread_clipmerge ) {
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ch_input_for_fastp = reads
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.dump(tag: "pre-fastp_branch")
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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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ch_input_for_fastp.single.dump(tag: "input_fastp_single")
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ch_input_for_fastp.paired.dump(tag: "input_fastp_paired")
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FASTP_SINGLE ( ch_input_for_fastp.single, false, false )
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FASTP_PAIRED ( ch_input_for_fastp.paired, false, true )
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ch_fastp_reads_prepped = FASTP_PAIRED.out.reads_merged
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.mix( FASTP_SINGLE.out.reads )
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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'] = 1
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[ meta_new, reads ]
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}
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FASTQC_POST ( ch_fastp_reads_prepped )
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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( FASTQC_POST.out.zip.collect{it[1]} )
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ch_multiqc_files = ch_multiqc_files.mix( FASTP_SINGLE.out.json.collect{it[1]} )
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ch_multiqc_files = ch_multiqc_files.mix( FASTP_PAIRED.out.json.collect{it[1]} )
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ch_multiqc_files.dump(tag: "preprocessing_mqc_final")
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} else {
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ch_processed_reads = reads
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}
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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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