From 9a588dd5682ff531c8b60fe2a4bb650a7638b4d6 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 13 Apr 2021 17:52:06 +0200
Subject: [PATCH] kallisto: update file to match CONTRIBUTING.md
---
src/nf_modules/kallisto/main.nf | 40 +++++++++++++++++++++++----------
1 file changed, 28 insertions(+), 12 deletions(-)
diff --git a/src/nf_modules/kallisto/main.nf b/src/nf_modules/kallisto/main.nf
index 2a0c1ed1..19087331 100644
--- a/src/nf_modules/kallisto/main.nf
+++ b/src/nf_modules/kallisto/main.nf
@@ -2,17 +2,21 @@ version = "0.44.0"
container_url = "lbmc/kallisto:${version}"
params.index_fasta = "-k 31 --make-unique"
+params.index_fasta_out = ""
process index_fasta {
container = "${container_url}"
label "big_mem_multi_cpus"
- tag "$fasta.baseName"
+ tag "$file_id"
+ if (params.index_fasta_out != "") {
+ publishDir "results/${params.index_fasta_out}", mode: 'copy'
+ }
input:
- path fasta
+ tuble val(file_id), path(fasta)
output:
- path "*.index*", emit: index
- path "*_report.txt", emit: report
+ tuple val(file_id), path("*.index*"), emit: index
+ tuple val(file_id), path("*_report.txt"), emit: report
script:
"""
@@ -22,18 +26,22 @@ kallisto index ${params.index_fasta} -i ${fasta.baseName}.index ${fasta} \
}
params.mapping_fastq = "--bias --bootstrap-samples 100"
+params.mapping_fastq_out = ""
process mapping_fastq {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$pair_id"
+ if (params.mapping_fastq_out != "") {
+ publishDir "results/${params.mapping_fastq_out}", mode: 'copy'
+ }
input:
- path index
+ tuple val(index_id), path(index)
tuple val(pair_id), path(reads)
output:
- path "${pair_id}", emit: counts
- path "*_report.txt", emit: report
+ tuple val(pair_id), path("${pair_id}"), emit: counts
+ tuple val(pair_id), path("*_report.txt"), emit: report
script:
@@ -55,18 +63,22 @@ ${reads} &> ${reads.simpleName}_kallisto_mapping_report.txt
}
params.mapping_fastq_pairedend = "--bias --bootstrap-samples 100"
+params.mapping_fastq_pairedend_out = ""
process mapping_fastq_pairedend {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$pair_id"
+ if (params.mapping_fastq_pairedend_out != "") {
+ publishDir "results/${params.mapping_fastq_pairedend_out}", mode: 'copy'
+ }
input:
- path index
+ tuple val(index_id), path(index)
tuple val(pair_id), path(reads)
output:
- path "${pair_id}", emit: counts
- path "*_report.txt", emit: report
+ tuple val(pair_id), path("${pair_id}"), emit: counts
+ tuple val(pair_id), path("*_report.txt"), emit: report
script:
"""
@@ -79,18 +91,22 @@ ${reads[0]} ${reads[1]} &> ${pair_id}_kallisto_mapping_report.txt
params.mapping_fastq_singleend = "--bias --bootstrap-samples 100"
+params.mapping_fastq_singleend_out = ""
process mapping_fastq_singleend {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$file_id"
+ if (params.mapping_fastq_singleend_out != "") {
+ publishDir "results/${params.mapping_fastq_singleend_out}", mode: 'copy'
+ }
input:
- path index
+ tuple val(index_id), path(index)
tuple val(file_id), path(reads)
output:
tuple val(file_id), path("${pair_id}"), emit: counts
- path "*_report.txt", emit: report
+ tuple val(file_id), path("*_report.txt"), emit: report
script:
"""
--
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