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taxprofiler/subworkflows/local/longread_preprocessing.nf

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//
// Process long raw reads with porechop
//
include { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/fastqc/main'
include { FALCO as FALCO_PROCESSED } from '../../modules/nf-core/falco/main'
include { PORECHOP } from '../../modules/nf-core/porechop/main'
include { FILTLONG } from '../../modules/nf-core/filtlong/main'
workflow LONGREAD_PREPROCESSING {
take:
reads
main:
ch_versions = Channel.empty()
ch_multiqc_files = Channel.empty()
if ( !params.longread_qc_skipadaptertrim && params.longread_qc_skipqualityfilter) {
PORECHOP ( reads )
ch_processed_reads = PORECHOP.out.reads
.map {
meta, reads ->
def meta_new = meta.clone()
meta_new['single_end'] = 1
[ meta_new, reads ]
}
ch_versions = ch_versions.mix(PORECHOP.out.versions.first())
ch_multiqc_files = ch_multiqc_files.mix( PORECHOP.out.log )
} else if ( params.longread_qc_skipadaptertrim && !params.longread_qc_skipqualityfilter) {
ch_processed_reads = FILTLONG ( reads.map{ meta, reads -> [meta, [], reads ]} )
ch_versions = ch_versions.mix(FILTLONG.out.versions.first())
ch_multiqc_files = ch_multiqc_files.mix( FILTLONG.out.log )
} else {
PORECHOP ( reads )
ch_clipped_reads = PORECHOP.out.reads
.map {
meta, reads ->
def meta_new = meta.clone()
meta_new['single_end'] = 1
[ meta_new, reads ]
}
ch_processed_reads = FILTLONG ( ch_clipped_reads.map{ meta, reads -> [meta, [], reads ]} ).reads
ch_versions = ch_versions.mix(PORECHOP.out.versions.first())
ch_versions = ch_versions.mix(FILTLONG.out.versions.first())
ch_multiqc_files = ch_multiqc_files.mix( PORECHOP.out.log )
ch_multiqc_files = ch_multiqc_files.mix( FILTLONG.out.log )
}
if (params.preprocessing_qc_tool == 'fastqc') {
FASTQC_PROCESSED ( ch_processed_reads )
ch_versions = ch_versions.mix( FASTQC_PROCESSED.out.versions )
ch_multiqc_files = ch_multiqc_files.mix( FASTQC_PROCESSED.out.zip )
} else if (params.preprocessing_qc_tool == 'falco') {
FALCO_PROCESSED ( ch_processed_reads )
ch_versions = ch_versions.mix( FALCO_PROCESSED.out.versions )
ch_multiqc_files = ch_multiqc_files.mix( FALCO_PROCESSED.out.txt )
}
emit:
reads = ch_processed_reads // channel: [ val(meta), [ reads ] ]
versions = ch_versions // channel: [ versions.yml ]
mqc = ch_multiqc_files
}