Commit 0f0fc8d7 authored by lrodrig1's avatar lrodrig1
Browse files

add publishDir on bam filtering subworkflow in Nextflow

parent 2f365102
params.bamsDir = ""
process SAMTOOLS_INDEX {
tag { "samtools index" }
container 'quay.io/biocontainers/samtools:1.5--2'
publishDir "${params.outputDir}/${params.bamsDir}", enabled: params.bamsDir, mode: 'copy'
input:
path input
......
params.bamsDir = "output_bams"
/*
* Include for bam_filtering
*/
......@@ -6,7 +8,7 @@ include {
} from "../modules/samtools_view"
include {
SAMTOOLS_INDEX
} from "../modules/samtools_index"
} from "../modules/samtools_index" params([*:params, "bamsDir": ""])
/*
......
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