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34 lines
1.1 KiB
Text
34 lines
1.1 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/modules/bowtie2/build/main'
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include { BOWTIE2_ALIGN } from '../../modules/nf-core/modules/bowtie2/align/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 )
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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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emit:
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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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