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Add bowtie2 mapped reads
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commit
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1 changed files with 16 additions and 5 deletions
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@ -4,8 +4,9 @@
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include { BOWTIE2_BUILD } from '../../modules/nf-core/bowtie2/build/main'
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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 { 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_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_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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workflow SHORTREAD_HOSTREMOVAL {
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take:
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take:
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@ -28,9 +29,19 @@ workflow SHORTREAD_HOSTREMOVAL {
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ch_versions = ch_versions.mix( BOWTIE2_ALIGN.out.versions.first() )
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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_multiqc_files = ch_multiqc_files.mix( BOWTIE2_ALIGN.out.log )
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SAMTOOLS_INDEX ( BOWTIE2_ALIGN.out.bam )
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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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bam_bai = BOWTIE2_ALIGN.out.bam
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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 = SAMTOOLS_VIEW.out.bam
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.join(SAMTOOLS_INDEX.out.bai, remainder: true)
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.join(SAMTOOLS_INDEX.out.bai, remainder: true)
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SAMTOOLS_STATS ( bam_bai, reference )
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SAMTOOLS_STATS ( bam_bai, reference )
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