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73 lines
3.1 KiB
Text
73 lines
3.1 KiB
Text
//
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// Process long raw reads with porechop
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//
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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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include { PORECHOP_PORECHOP } from '../../modules/nf-core/porechop/porechop/main'
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include { FILTLONG } from '../../modules/nf-core/filtlong/main'
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workflow LONGREAD_PREPROCESSING {
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take:
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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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if ( !params.longread_qc_skipadaptertrim && params.longread_qc_skipqualityfilter) {
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PORECHOP_PORECHOP ( reads )
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ch_processed_reads = PORECHOP_PORECHOP.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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ch_versions = ch_versions.mix(PORECHOP_PORECHOP.out.versions.first())
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ch_multiqc_files = ch_multiqc_files.mix( PORECHOP_PORECHOP.out.log )
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} else if ( params.longread_qc_skipadaptertrim && !params.longread_qc_skipqualityfilter) {
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ch_processed_reads = FILTLONG ( reads.map{ meta, reads -> [meta, [], reads ]} )
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ch_versions = ch_versions.mix(FILTLONG.out.versions.first())
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ch_multiqc_files = ch_multiqc_files.mix( FILTLONG.out.log )
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} else {
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PORECHOP_PORECHOP ( reads )
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ch_clipped_reads = PORECHOP_PORECHOP.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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ch_processed_reads = FILTLONG ( ch_clipped_reads.map{ meta, reads -> [meta, [], reads ]} ).reads
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ch_versions = ch_versions.mix(PORECHOP_PORECHOP.out.versions.first())
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ch_versions = ch_versions.mix(FILTLONG.out.versions.first())
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ch_multiqc_files = ch_multiqc_files.mix( PORECHOP_PORECHOP.out.log )
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ch_multiqc_files = ch_multiqc_files.mix( FILTLONG.out.log )
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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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