millironx/taxprofiler
1
0
Fork 0
mirror of https://github.com/MillironX/taxprofiler.git synced 2024-12-22 15:28:16 +00:00
Code Issues Releases Packages Activity

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

Browse source 
Include the mapped reads in samtools stats
This commit is contained in:
Sofia Stamouli 2022-11-23 10:21:47 +01:00 committed by GitHub
commit f8b769a8f0
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
2 changed files with 3 additions and 3 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

2
subworkflows/local/longread_hostremoval.nf
View file

@ -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 )

4
subworkflows/local/shortread_hostremoval.nf
View file

@ -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 )