mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-22 11:39:54 +00:00
42 lines
1.4 KiB
Text
42 lines
1.4 KiB
Text
//
|
|
// Check input samplesheet and get read channels
|
|
//
|
|
|
|
|
|
include { SHORTREAD_FASTP } from './shortread_fastp'
|
|
include { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/modules/fastqc/main'
|
|
|
|
workflow SHORTREAD_PREPROCESSING {
|
|
take:
|
|
reads // file: /path/to/samplesheet.csv
|
|
|
|
main:
|
|
ch_versions = Channel.empty()
|
|
ch_multiqc_files = Channel.empty()
|
|
|
|
//
|
|
// STEP: Read clipping and merging
|
|
//
|
|
// TODO give option to clip only and retain pairs
|
|
// TODO give option to retain singletons (probably fastp option likely)
|
|
// TODO move to subworkflow
|
|
|
|
if ( params.shortread_clipmerge_tool == "fastp" ) {
|
|
ch_processed_reads = SHORTREAD_FASTP ( reads ).reads
|
|
ch_versions = ch_versions.mix( SHORTREAD_FASTP.out.versions )
|
|
ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_FASTP.out.mqc )
|
|
} else {
|
|
ch_processed_reads = reads
|
|
}
|
|
|
|
//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.collect{it[1]} )
|
|
|
|
emit:
|
|
// TODO: problem, this is being exported as a multi-channel output? This is why FASTQC is broken
|
|
reads = ch_processed_reads // channel: [ val(meta), [ reads ] ]
|
|
versions = ch_versions // channel: [ versions.yml ]
|
|
mqc = ch_multiqc_files
|
|
}
|
|
|