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48 lines
1.6 KiB
Text
48 lines
1.6 KiB
Text
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//
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// Remove host reads via alignment and export off-target reads
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//
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include { MINIMAP2_INDEX } from '../../modules/nf-core/modules/minimap2/index/main'
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include { MINIMAP2_ALIGN } from '../../modules/nf-core/modules/minimap2/align/main'
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include { SAMTOOLS_VIEW } from '../../modules/nf-core/modules/samtools/view/main'
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include { SAMTOOLS_BAM2FQ } from '../../modules/nf-core/modules/samtools/bam2fq/main'
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workflow LONGREAD_HOSTREMOVAL {
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take:
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reads // [ [ meta ], [ reads ] ]
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reference // /path/to/fasta
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index // /path/to/index
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main:
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ch_versions = Channel.empty()
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ch_multiqc_files = Channel.empty()
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if ( !params.longread_hostremoval_index ) {
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ch_minimap2_index = MINIMAP2_INDEX ( reference ).index
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ch_versions = ch_versions.mix( MINIMAP2_INDEX.out.versions )
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} else {
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ch_minimap2_index = index
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}
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MINIMAP2_ALIGN ( reads, ch_minimap2_index, true, false, false )
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ch_versions = ch_versions.mix( MINIMAP2_ALIGN.out.versions.first() )
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ch_minimap2_mapped = MINIMAP2_ALIGN.out.bam
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.map {
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meta, reads ->
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[ meta, reads, [] ]
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}
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SAMTOOLS_VIEW ( ch_minimap2_mapped , [] )
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ch_versions = ch_versions.mix( SAMTOOLS_VIEW.out.versions.first() )
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SAMTOOLS_BAM2FQ ( SAMTOOLS_VIEW.out.bam, false )
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ch_versions = ch_versions.mix( SAMTOOLS_BAM2FQ.out.versions.first() )
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emit:
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reads = SAMTOOLS_BAM2FQ.out.reads // channel: [ val(meta), [ reads ] ]
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versions = ch_versions // channel: [ versions.yml ]
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}
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