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47 lines
1.8 KiB
Text
47 lines
1.8 KiB
Text
//
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// Perform read trimming and merging
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//
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include { SHORTREAD_FASTP } from './shortread_fastp'
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include { SHORTREAD_ADAPTERREMOVAL } from './shortread_adapterremoval'
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include { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/fastqc/main'
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include { FALCO as FALCO_PROCESSED } from '../../modules/nf-core/falco/main'
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workflow SHORTREAD_PREPROCESSING {
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take:
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reads // [ [ meta ], [ reads ] ]
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adapterlist // file
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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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if ( params.shortread_qc_tool == "fastp" ) {
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ch_processed_reads = SHORTREAD_FASTP ( reads, adapterlist ).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 if ( params.shortread_qc_tool == "adapterremoval" ) {
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ch_processed_reads = SHORTREAD_ADAPTERREMOVAL ( reads, adapterlist ).reads
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ch_versions = ch_versions.mix( SHORTREAD_ADAPTERREMOVAL.out.versions )
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ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_ADAPTERREMOVAL.out.mqc )
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} else {
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ch_processed_reads = reads
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}
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if (params.preprocessing_qc_tool == 'fastqc') {
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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 )
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} else if (params.preprocessing_qc_tool == 'falco') {
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FALCO_PROCESSED ( ch_processed_reads )
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ch_versions = ch_versions.mix( FALCO_PROCESSED.out.versions )
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ch_multiqc_files = ch_multiqc_files.mix( FALCO_PROCESSED.out.txt )
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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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