mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-14 07:23:08 +00:00
47 lines
1.6 KiB
Text
47 lines
1.6 KiB
Text
//
|
|
// Remove host reads via alignment and export off-target reads
|
|
//
|
|
|
|
include { MINIMAP2_INDEX } from '../../modules/nf-core/modules/minimap2/index/main'
|
|
include { MINIMAP2_ALIGN } from '../../modules/nf-core/modules/minimap2/align/main'
|
|
include { SAMTOOLS_VIEW } from '../../modules/nf-core/modules/samtools/view/main'
|
|
include { SAMTOOLS_BAM2FQ } from '../../modules/nf-core/modules/samtools/bam2fq/main'
|
|
|
|
workflow LONGREAD_HOSTREMOVAL {
|
|
take:
|
|
reads // [ [ meta ], [ reads ] ]
|
|
reference // /path/to/fasta
|
|
index // /path/to/index
|
|
|
|
main:
|
|
ch_versions = Channel.empty()
|
|
ch_multiqc_files = Channel.empty()
|
|
|
|
if ( !params.longread_hostremoval_index ) {
|
|
ch_minimap2_index = MINIMAP2_INDEX ( reference ).index
|
|
ch_versions = ch_versions.mix( MINIMAP2_INDEX.out.versions )
|
|
} else {
|
|
ch_minimap2_index = index
|
|
}
|
|
|
|
MINIMAP2_ALIGN ( reads, ch_minimap2_index, true, false, false )
|
|
ch_versions = ch_versions.mix( MINIMAP2_ALIGN.out.versions.first() )
|
|
ch_minimap2_mapped = MINIMAP2_ALIGN.out.bam
|
|
.map {
|
|
meta, reads ->
|
|
[ meta, reads, [] ]
|
|
}
|
|
|
|
|
|
SAMTOOLS_VIEW ( ch_minimap2_mapped , [] )
|
|
ch_versions = ch_versions.mix( SAMTOOLS_VIEW.out.versions.first() )
|
|
|
|
SAMTOOLS_BAM2FQ ( SAMTOOLS_VIEW.out.bam, false )
|
|
ch_versions = ch_versions.mix( SAMTOOLS_BAM2FQ.out.versions.first() )
|
|
|
|
|
|
emit:
|
|
reads = SAMTOOLS_BAM2FQ.out.reads // channel: [ val(meta), [ reads ] ]
|
|
versions = ch_versions // channel: [ versions.yml ]
|
|
}
|
|
|