Commit 2f365102 authored by lrodrig1's avatar lrodrig1
Browse files

minor changes to bam filtering in Nextflow

parent dfb2162d
process SAMTOOLS_VIEW {
tag 'samtools view'
tag { "samtools view" }
container 'quay.io/biocontainers/samtools:1.5--2'
input:
path input
output:
path '*.filtered.bam', emit: output
path '*.filtered.bam'
script:
def min_mapping_qualityArgument = params.min_mapping_quality ? "-q $params.min_mapping_quality" : ''
......
......@@ -10,16 +10,16 @@ include {
/*
* Subworkflow bam_filtering
* Subworkflow bam_filtering
*/
workflow SUB_BAM_FILTERING {
take:
input
input
main:
SAMTOOLS_VIEW( input )
SAMTOOLS_INDEX( SAMTOOLS_VIEW.out )
SAMTOOLS_VIEW(input)
SAMTOOLS_INDEX(SAMTOOLS_VIEW.out)
emit:
output = SAMTOOLS_INDEX.out
}
\ No newline at end of file
bams = SAMTOOLS_INDEX.out
}
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