1
0
Fork 0
mirror of https://github.com/MillironX/taxprofiler.git synced 2024-11-11 00:43:10 +00:00
taxprofiler/subworkflows/local/longread_hostremoval.nf

63 lines
2.3 KiB
Text
Raw Normal View History

2022-05-03 07:34:27 +00:00
//
// Remove host reads via alignment and export off-target reads
//
include { MINIMAP2_INDEX } from '../../modules/nf-core/minimap2/index/main'
include { MINIMAP2_ALIGN } from '../../modules/nf-core/minimap2/align/main'
include { SAMTOOLS_VIEW } from '../../modules/nf-core/samtools/view/main'
include { SAMTOOLS_BAM2FQ } from '../../modules/nf-core/samtools/bam2fq/main'
2022-10-28 09:40:50 +00:00
include { SAMTOOLS_INDEX } from '../../modules/nf-core/samtools/index/main'
include { SAMTOOLS_STATS } from '../../modules/nf-core/samtools/stats/main'
2022-05-03 07:34:27 +00:00
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 ) {
2022-10-11 10:38:18 +00:00
ch_minimap2_index = MINIMAP2_INDEX ( [ [], reference ] ).index.map { it[1] }
2022-05-03 07:34:27 +00:00
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, [] ]
}
2022-10-05 11:49:35 +00:00
SAMTOOLS_VIEW ( ch_minimap2_mapped , [], [] )
2022-05-03 07:34:27 +00:00
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() )
2022-10-28 09:40:50 +00:00
SAMTOOLS_INDEX ( SAMTOOLS_VIEW.out.bam )
ch_versions = ch_versions.mix( SAMTOOLS_INDEX.out.versions.first() )
SAMTOOLS_VIEW.out.bam
.join(SAMTOOLS_INDEX.out.bai, by: [0], remainder: true)
.set { bam_bai }
SAMTOOLS_STATS ( bam_bai, reference )
ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions.first())
ch_multiqc_files = ch_multiqc_files.mix( SAMTOOLS_STATS.out.stats )
2022-05-03 07:34:27 +00:00
emit:
2022-10-28 09:40:50 +00:00
stats = SAMTOOLS_STATS.out.stats //channel: [val(meta), [reads ] ]
2022-05-03 07:34:27 +00:00
reads = SAMTOOLS_BAM2FQ.out.reads // channel: [ val(meta), [ reads ] ]
versions = ch_versions // channel: [ versions.yml ]
2022-10-28 09:40:50 +00:00
mqc = ch_multiqc_files
2022-05-03 07:34:27 +00:00
}