mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-13 07:23:10 +00:00
Merge pull request #172 from genomic-medicine-sweden/update_samtools_stats
Include the mapped reads in samtools stats
This commit is contained in:
commit
f8b769a8f0
2 changed files with 3 additions and 3 deletions
|
@ -44,7 +44,7 @@ workflow LONGREAD_HOSTREMOVAL {
|
|||
SAMTOOLS_INDEX ( SAMTOOLS_VIEW.out.bam )
|
||||
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)
|
||||
|
||||
SAMTOOLS_STATS ( bam_bai, reference )
|
||||
|
|
|
@ -25,7 +25,7 @@ workflow SHORTREAD_HOSTREMOVAL {
|
|||
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_multiqc_files = ch_multiqc_files.mix( BOWTIE2_ALIGN.out.log )
|
||||
|
||||
|
@ -41,7 +41,7 @@ workflow SHORTREAD_HOSTREMOVAL {
|
|||
SAMTOOLS_INDEX ( SAMTOOLS_VIEW.out.bam )
|
||||
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)
|
||||
|
||||
SAMTOOLS_STATS ( bam_bai, reference )
|
||||
|
|
Loading…
Reference in a new issue