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42 lines
1.4 KiB
Text
42 lines
1.4 KiB
Text
//
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// Check input samplesheet and get read channels
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//
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include { SHORTREAD_FASTP } from './shortread_fastp'
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include { FASTQC as FASTQC_PROCESSED } 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_tool == "fastp" ) {
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ch_processed_reads = SHORTREAD_FASTP ( reads ).reads
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ch_versions = ch_versions.mix( SHORTREAD_FASTP.out.versions )
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ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_FASTP.out.mqc )
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} else {
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ch_processed_reads = reads
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}
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//FASTQC_PROCESSED ( ch_processed_reads )
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//ch_versions = ch_versions.mix( FASTQC_PROCESSED.out.versions )
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//ch_multiqc_files = ch_multiqc_files.mix( FASTQC_PROCESSED.out.zip.collect{it[1]} )
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emit:
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// TODO: problem, this is being exported as a multi-channel output? This is why FASTQC is broken
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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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