From 8338d66f2ddb53057bb7c21d493162674142f51c Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Mon, 25 Jan 2021 16:51:03 +0100
Subject: [PATCH] bedtools: fix bam_to_fastq script
---
src/nf_modules/bedtools/main.nf | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/src/nf_modules/bedtools/main.nf b/src/nf_modules/bedtools/main.nf
index 8aaddf5c..22361ed8 100644
--- a/src/nf_modules/bedtools/main.nf
+++ b/src/nf_modules/bedtools/main.nf
@@ -25,7 +25,7 @@ process bam_to_fastq_singleend {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "${bam.baseName}"
- publishDir "results/fasta/", mode: 'copy'
+ publishDir "results/mapping/fastq/", mode: 'copy'
input:
path bam
@@ -35,7 +35,7 @@ process bam_to_fastq_singleend {
script:
"""
-bedtools bamtofastq
+bedtools bamtofastq \
-i ${bam} -fq ${bam.baseName}.fastq
"""
}
@@ -44,7 +44,7 @@ process bam_to_fastq_pairedend {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "${bam.baseName}"
- publishDir "results/fasta/", mode: 'copy'
+ publishDir "results/mapping/fastq/", mode: 'copy'
input:
path bam
@@ -54,7 +54,7 @@ process bam_to_fastq_pairedend {
script:
"""
-bedtools bamtofastq
+bedtools bamtofastq \
-i ${bam} -fq ${bam.baseName}_R1.fastq -fq2 ${bam.baseName}_R2.fastq
"""
}
--
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