From e4d6d7ab5bd4d993b24807db8bfe8ae7a69891d0 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 7 Oct 2021 11:20:05 +0200
Subject: [PATCH] samtools: add rm_from_bam process
---
src/nf_modules/samtools/main.nf | 22 ++++++++++++++++++++++
1 file changed, 22 insertions(+)
diff --git a/src/nf_modules/samtools/main.nf b/src/nf_modules/samtools/main.nf
index 3c940314..0d384315 100644
--- a/src/nf_modules/samtools/main.nf
+++ b/src/nf_modules/samtools/main.nf
@@ -74,6 +74,28 @@ samtools view -@ ${task.cpus} -hb ${bam} -L ${bed} ${params.filter_bam} > \
"""
}
+params.rm_from_bam = ""
+params.rm_from_bam_out = ""
+process filter_bam {
+ container = "${container_url}"
+ label "big_mem_multi_cpus"
+ tag "$file_id"
+ if (params.rm_from_bam_out != "") {
+ publishDir "results/${params.rm_from_bam_out}", mode: 'copy'
+ }
+
+ input:
+ tuple val(file_id), path(bam)
+ tuple val(bed_id), path(bed)
+
+ output:
+ tuple val(file_id), path("*_filtered.bam"), emit: bam
+ script:
+"""
+samtools view -@ ${task.cpus} ${params.filter_bam} -hb -L ${bed} -U ${bam.simpleName}_filtered.bam ${bam} > /dev/null
+"""
+}
+
params.filter_bam_mapped = "-F 4"
params.filter_bam_mapped_out = ""
process filter_bam_mapped {
--
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