From 84daa85860c77ccf3353e652fb0adfdea5f91857 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 14 Apr 2021 18:35:25 +0200
Subject: [PATCH] samtools: update to follow CONTRIBUTING.md
---
src/nf_modules/bedtools/main.nf | 2 +-
src/nf_modules/samtools/main.nf | 6 +++---
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/src/nf_modules/bedtools/main.nf b/src/nf_modules/bedtools/main.nf
index 7f986685..9400abf4 100644
--- a/src/nf_modules/bedtools/main.nf
+++ b/src/nf_modules/bedtools/main.nf
@@ -2,7 +2,7 @@ version = "2.25.0"
container_url = "lbmc/bedtools:${version}"
params.fasta_from_bed = "-name"
-params.fasta_from_bed_out = "-name"
+params.fasta_from_bed_out = ""
process fasta_from_bed {
container = "${container_url}"
label "big_mem_mono_cpus"
diff --git a/src/nf_modules/samtools/main.nf b/src/nf_modules/samtools/main.nf
index 8143a814..b5d075de 100644
--- a/src/nf_modules/samtools/main.nf
+++ b/src/nf_modules/samtools/main.nf
@@ -44,7 +44,7 @@ process filter_bam {
input:
tuple val(file_id), path(bam)
- path bed
+ tuple val(bed_id), path(bed)
output:
tuple val(file_id), path("*_filtered.bam"), emit: bam
@@ -208,7 +208,7 @@ process flagstat_2_multiqc {
tuple val(file_id), path(tsv)
output:
- path "*.txt" , emit: report
+ tuple val(file_id), path("*.txt"), emit: report
"""
mv ${tsv} ${tsv.simpleName}.flagstat.txt
"""
@@ -221,7 +221,7 @@ process idxstat_2_multiqc {
tuple val(file_id), path(tsv)
output:
- path "*.txt", emit: report
+ tuple val(file_id), path("*.txt"), emit: report
"""
mv ${tsv} ${tsv.simpleName}.idxstats.txt
"""
--
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