From 9f34d8460438b9c9967ee940ae088e96e4ba0bed Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Mon, 25 Jan 2021 16:46:33 +0100
Subject: [PATCH] samtools: fix catched bams names
---
src/nf_modules/samtools/main.nf | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/src/nf_modules/samtools/main.nf b/src/nf_modules/samtools/main.nf
index 3ebd134d..f1ff8dc8 100644
--- a/src/nf_modules/samtools/main.nf
+++ b/src/nf_modules/samtools/main.nf
@@ -27,7 +27,7 @@ process filter_bam_mapped {
tuple val(file_id), path(bam)
output:
- tuple val(file_id), path("*_filtered.bam"), emit: bam
+ tuple val(file_id), path("*_mapped.bam"), emit: bam
script:
"""
samtools view -@ ${task.cpus} -F 4 -hb ${bam} -L ${bed} > ${file_id}_mapped.bam
@@ -43,7 +43,7 @@ process filter_bam_unmapped {
tuple val(file_id), path(bam)
output:
- tuple val(file_id), path("*_filtered.bam"), emit: bam
+ tuple val(file_id), path("*_unmapped.bam"), emit: bam
script:
"""
samtools view -@ ${task.cpus} -f 4 -hb ${bam} > ${file_id}_unmapped.bam
--
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