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Merge pull request #172 from genomic-medicine-sweden/update_samtools_stats

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Include the mapped reads in samtools stats
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Sofia Stamouli 2022-11-23 10:21:47 +01:00 committed by GitHub
commit f8b769a8f0
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GPG key ID: 4AEE18F83AFDEB23
2 changed files with 3 additions and 3 deletions
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2
subworkflows/local/longread_hostremoval.nf
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@ -44,7 +44,7 @@ workflow LONGREAD_HOSTREMOVAL {
SAMTOOLS_INDEX ( SAMTOOLS_VIEW.out.bam ) SAMTOOLS_INDEX ( SAMTOOLS_VIEW.out.bam )
ch_versions = ch_versions.mix( SAMTOOLS_INDEX.out.versions.first() ) ch_versions = ch_versions.mix( SAMTOOLS_INDEX.out.versions.first() )
bam_bai = SAMTOOLS_VIEW.out.bam bam_bai = MINIMAP2_ALIGN.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 )

4
subworkflows/local/shortread_hostremoval.nf
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@ -25,7 +25,7 @@ workflow SHORTREAD_HOSTREMOVAL {
ch_bowtie2_index = index.first() ch_bowtie2_index = index.first()
} }
BOWTIE2_ALIGN ( reads, ch_bowtie2_index, true, false ) BOWTIE2_ALIGN ( reads, ch_bowtie2_index, true, true)
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 )
@ -41,7 +41,7 @@ workflow SHORTREAD_HOSTREMOVAL {
SAMTOOLS_INDEX ( SAMTOOLS_VIEW.out.bam ) SAMTOOLS_INDEX ( SAMTOOLS_VIEW.out.bam )
ch_versions = ch_versions.mix( SAMTOOLS_INDEX.out.versions.first() ) ch_versions = ch_versions.mix( SAMTOOLS_INDEX.out.versions.first() )
bam_bai = SAMTOOLS_VIEW.out.bam bam_bai = BOWTIE2_ALIGN.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 )