You cannot select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
48 lines
1.8 KiB
Plaintext
48 lines
1.8 KiB
Plaintext
//
|
|
// Perform read trimming and merging
|
|
//
|
|
|
|
|
|
include { SHORTREAD_FASTP } from './shortread_fastp'
|
|
include { SHORTREAD_ADAPTERREMOVAL } from './shortread_adapterremoval'
|
|
include { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/fastqc/main'
|
|
include { FALCO as FALCO_PROCESSED } from '../../modules/nf-core/falco/main'
|
|
|
|
workflow SHORTREAD_PREPROCESSING {
|
|
take:
|
|
reads // [ [ meta ], [ reads ] ]
|
|
adapterlist // file
|
|
|
|
main:
|
|
ch_versions = Channel.empty()
|
|
ch_multiqc_files = Channel.empty()
|
|
|
|
if ( params.shortread_qc_tool == "fastp" ) {
|
|
ch_processed_reads = SHORTREAD_FASTP ( reads, adapterlist ).reads
|
|
ch_versions = ch_versions.mix( SHORTREAD_FASTP.out.versions )
|
|
ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_FASTP.out.mqc )
|
|
} else if ( params.shortread_qc_tool == "adapterremoval" ) {
|
|
ch_processed_reads = SHORTREAD_ADAPTERREMOVAL ( reads, adapterlist ).reads
|
|
ch_versions = ch_versions.mix( SHORTREAD_ADAPTERREMOVAL.out.versions )
|
|
ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_ADAPTERREMOVAL.out.mqc )
|
|
} else {
|
|
ch_processed_reads = reads
|
|
}
|
|
|
|
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
|
|
}
|
|
|