From 8bebb4a1d11b33a0d249aded27342e2e4b3110fa Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Mon, 25 Jan 2021 16:26:53 +0100
Subject: [PATCH] fix input and output for bedtools and samtools
---
src/nf_modules/bedtools/main.nf | 10 ++++------
src/nf_modules/samtools/main.nf | 2 --
2 files changed, 4 insertions(+), 8 deletions(-)
diff --git a/src/nf_modules/bedtools/main.nf b/src/nf_modules/bedtools/main.nf
index 70314d7c..ebf68937 100644
--- a/src/nf_modules/bedtools/main.nf
+++ b/src/nf_modules/bedtools/main.nf
@@ -28,11 +28,10 @@ process bam_to_fastq_singleend {
publishDir "results/fasta/", mode: 'copy'
input:
- path fasta
- path bed
+ path bam
output:
- path "*_extracted.fasta", emit: fasta
+ path "*.fastq", emit: fastq
script:
"""
@@ -48,11 +47,10 @@ process bam_to_fastq_paired_end {
publishDir "results/fasta/", mode: 'copy'
input:
- path fasta
- path bed
+ path bam
output:
- path "*_extracted.fasta", emit: fasta
+ path "*.fastq", emit: fasta
script:
"""
diff --git a/src/nf_modules/samtools/main.nf b/src/nf_modules/samtools/main.nf
index cf0d2158..83a5a177 100644
--- a/src/nf_modules/samtools/main.nf
+++ b/src/nf_modules/samtools/main.nf
@@ -25,7 +25,6 @@ process filter_bam_mapped {
input:
tuple val(file_id), path(bam)
- path bed
output:
tuple val(file_id), path("*_filtered.bam"), emit: bam
@@ -42,7 +41,6 @@ process filter_bam_unmapped {
input:
tuple val(file_id), path(bam)
- path bed
output:
tuple val(file_id), path("*_filtered.bam"), emit: bam
--
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