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Add bowtie2 mapped reads

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This commit is contained in:
Sofia Stamouli 2022-10-31 10:04:51 +01:00
parent c4a7d094c8
commit ce611d6efd
1 changed files with 16 additions and 5 deletions
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21
subworkflows/local/shortread_hostremoval.nf
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@ -4,8 +4,9 @@
include { BOWTIE2_BUILD } from '../../modules/nf-core/bowtie2/build/main' include { BOWTIE2_BUILD } from '../../modules/nf-core/bowtie2/build/main'
include { BOWTIE2_ALIGN } from '../../modules/nf-core/bowtie2/align/main' include { BOWTIE2_ALIGN } from '../../modules/nf-core/bowtie2/align/main'
include { SAMTOOLS_INDEX } from '../../modules/nf-core/samtools/index/main' include { SAMTOOLS_INDEX } from '../../modules/nf-core/samtools/index/main'
include { SAMTOOLS_STATS } from '../../modules/nf-core/samtools/stats/main' include { SAMTOOLS_STATS } from '../../modules/nf-core/samtools/stats/main'
include { SAMTOOLS_VIEW } from '../../modules/nf-core/samtools/view/main'
workflow SHORTREAD_HOSTREMOVAL { workflow SHORTREAD_HOSTREMOVAL {
take: take:
@ -28,9 +29,19 @@ workflow SHORTREAD_HOSTREMOVAL {
ch_versions = ch_versions.mix( BOWTIE2_ALIGN.out.versions.first() ) ch_versions = ch_versions.mix( BOWTIE2_ALIGN.out.versions.first() )
ch_multiqc_files = ch_multiqc_files.mix( BOWTIE2_ALIGN.out.log ) ch_multiqc_files = ch_multiqc_files.mix( BOWTIE2_ALIGN.out.log )
SAMTOOLS_INDEX ( BOWTIE2_ALIGN.out.bam ) ch_bowtie2_mapped = BOWTIE2_ALIGN.out.bam
.map {
meta, reads ->
[ meta, reads, [] ]
}
bam_bai = BOWTIE2_ALIGN.out.bam SAMTOOLS_VIEW ( ch_bowtie2_mapped, [], [] )
ch_versions = ch_versions.mix( SAMTOOLS_VIEW.out.versions.first() )
SAMTOOLS_INDEX ( SAMTOOLS_VIEW.out.bam )
ch_versions = ch_versions.mix( SAMTOOLS_INDEX.out.versions.first() )
bam_bai = SAMTOOLS_VIEW.out.bam
.join(SAMTOOLS_INDEX.out.bai, remainder: true) .join(SAMTOOLS_INDEX.out.bai, remainder: true)
SAMTOOLS_STATS ( bam_bai, reference ) SAMTOOLS_STATS ( bam_bai, reference )
@ -38,7 +49,7 @@ workflow SHORTREAD_HOSTREMOVAL {
ch_multiqc_files = ch_multiqc_files.mix( SAMTOOLS_STATS.out.stats ) ch_multiqc_files = ch_multiqc_files.mix( SAMTOOLS_STATS.out.stats )
emit: emit:
stats = SAMTOOLS_STATS.out.stats stats = SAMTOOLS_STATS.out.stats
reads = BOWTIE2_ALIGN.out.fastq // channel: [ val(meta), [ reads ] ] reads = BOWTIE2_ALIGN.out.fastq // channel: [ val(meta), [ reads ] ]
versions = ch_versions // channel: [ versions.yml ] versions = ch_versions // channel: [ versions.yml ]
mqc = ch_multiqc_files mqc = ch_multiqc_files