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34 lines
1.2 KiB
Plaintext
34 lines
1.2 KiB
Plaintext
//
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// Check input samplesheet and get read channels
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//
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include { BBMAP_BBDUK } from '../../modules/nf-core/bbmap/bbduk/main'
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include { PRINSEQPLUSPLUS } from '../../modules/nf-core/prinseqplusplus/main'
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workflow SHORTREAD_COMPLEXITYFILTERING {
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take:
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reads // [ [ meta ], [ reads ] ]
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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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// fastp complexity filtering is activated via modules.conf in shortread_preprocessing
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if ( params.shortread_complexityfilter_tool == 'bbduk' ) {
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ch_filtered_reads = BBMAP_BBDUK ( reads, [] ).reads
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ch_versions = ch_versions.mix( BBMAP_BBDUK.out.versions.first() )
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ch_multiqc_files = ch_multiqc_files.mix( BBMAP_BBDUK.out.log )
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} else if ( params.shortread_complexityfilter_tool == 'prinseqplusplus' ) {
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ch_filtered_reads = PRINSEQPLUSPLUS ( reads ).good_reads
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ch_versions = ch_versions.mix( PRINSEQPLUSPLUS.out.versions.first() )
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} else {
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ch_filtered_reads = reads
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}
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emit:
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reads = ch_filtered_reads // 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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