From 699cd563e665cc75e6f734d42fb0cfe64718c8e5 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 13 Apr 2021 17:56:09 +0200
Subject: [PATCH] bedtools: update to match CONTRIBUTING.md
---
src/nf_modules/bedtools/main.nf | 34 ++++++++++++++++++++++++++-------
1 file changed, 27 insertions(+), 7 deletions(-)
diff --git a/src/nf_modules/bedtools/main.nf b/src/nf_modules/bedtools/main.nf
index c8533656..284b7658 100644
--- a/src/nf_modules/bedtools/main.nf
+++ b/src/nf_modules/bedtools/main.nf
@@ -2,17 +2,21 @@ version = "2.25.0"
container_url = "lbmc/bedtools:${version}"
params.fasta_from_bed = "-name"
+params.fasta_from_bed_out = "-name"
process fasta_from_bed {
container = "${container_url}"
label "big_mem_mono_cpus"
- tag "${bed.baseName}"
+ tag "${file_id}"
+ if (params.fasta_from_bed_out != "") {
+ publishDir "results/${params.fasta_from_bed_out}", mode: 'copy'
+ }
input:
- path fasta
- path bed
+ tuple val(fasta_id), path(fasta)
+ tuple val(file_id), path(bed)
output:
- tuple val(bed.baseName), path("*_extracted.fasta"), emit: fasta
+ tuple val(bed_id), path("*_extracted.fasta"), emit: fasta
script:
"""
@@ -22,16 +26,20 @@ bedtools getfasta ${params.fasta_from_bed} \
}
params.merge_bed = ""
+params.merge_bed_out = ""
process merge_bed {
container = "${container_url}"
label "big_mem_mono_cpus"
- tag "${bed.baseName}"
+ tag "${file_id}"
+ if (params.merge_bed_out != "") {
+ publishDir "results/${params.merge_bed_out}", mode: 'copy'
+ }
input:
- path bed
+ tuple val(file_id), path(bed)
output:
- tuple val(bed[0].simpleName), path("*_merged.fasta"), emit: bed
+ tuple val(file_id), path("*_merged.fasta"), emit: bed
script:
"""
@@ -40,10 +48,14 @@ bedtools merge ${params.merge_bed} -i ${bed} > ${bed[0].simpleName}_merged.bed
}
params.bam_to_fastq_singleend = ""
+params.bam_to_fastq_singleend_out = ""
process bam_to_fastq_singleend {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "${bam_id}"
+ if (params.bam_to_fastq_singleend_out != "") {
+ publishDir "results/${params.bam_to_fastq_singleend_out}", mode: 'copy'
+ }
input:
tuple val(bam_id), path(bam)
@@ -60,10 +72,14 @@ bedtools bamtofastq \
}
params.bam_to_fastq_pairedend = ""
+params.bam_to_fastq_pairedend_out = ""
process bam_to_fastq_pairedend {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "${bam_id}"
+ if (params.bam_to_fastq_pairedend_out != "") {
+ publishDir "results/${params.bam_to_fastq_pairedend_out}", mode: 'copy'
+ }
input:
tuple val(bam_id), path(bam)
@@ -80,10 +96,14 @@ bedtools bamtofastq \
}
params.bam_to_bedgraph = ""
+params.bam_to_bedgraph_out = ""
process bam_to_bedgraph {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "${bam_id}"
+ if (params.bam_to_bedgraph_out != "") {
+ publishDir "results/${params.bam_to_bedgraph_out}", mode: 'copy'
+ }
input:
tuple val(bam_id), path(bam)
--
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