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57 lines
2 KiB
Text
57 lines
2 KiB
Text
//
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// Remove host reads via alignment and export off-target reads
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//
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include { BOWTIE2_BUILD } from '../../modules/nf-core/bowtie2/build/main'
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include { BOWTIE2_ALIGN } from '../../modules/nf-core/bowtie2/align/main'
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include { SAMTOOLS_INDEX } from '../../modules/nf-core/samtools/index/main'
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include { SAMTOOLS_STATS } from '../../modules/nf-core/samtools/stats/main'
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include { SAMTOOLS_VIEW } from '../../modules/nf-core/samtools/view/main'
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workflow SHORTREAD_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.shortread_hostremoval_index ) {
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ch_bowtie2_index = BOWTIE2_BUILD ( reference ).index
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ch_versions = ch_versions.mix( BOWTIE2_BUILD.out.versions )
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} else {
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ch_bowtie2_index = index.first()
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}
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BOWTIE2_ALIGN ( reads, ch_bowtie2_index, true, true)
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ch_versions = ch_versions.mix( BOWTIE2_ALIGN.out.versions.first() )
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ch_multiqc_files = ch_multiqc_files.mix( BOWTIE2_ALIGN.out.log )
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ch_bowtie2_mapped = BOWTIE2_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_bowtie2_mapped, [], [] )
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ch_versions = ch_versions.mix( SAMTOOLS_VIEW.out.versions.first() )
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SAMTOOLS_INDEX ( SAMTOOLS_VIEW.out.bam )
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ch_versions = ch_versions.mix( SAMTOOLS_INDEX.out.versions.first() )
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bam_bai = BOWTIE2_ALIGN.out.bam
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.join(SAMTOOLS_INDEX.out.bai, remainder: true)
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SAMTOOLS_STATS ( bam_bai, reference )
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ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions.first())
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ch_multiqc_files = ch_multiqc_files.mix( SAMTOOLS_STATS.out.stats )
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emit:
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stats = SAMTOOLS_STATS.out.stats
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reads = BOWTIE2_ALIGN.out.fastq // channel: [ val(meta), [ reads ] ]
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versions = ch_versions // channel: [ versions.yml ]
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mqc = ch_multiqc_files
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}
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