From be4657c776da9c7c6ca6198a6a96f585cb7bab6f Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 14 Apr 2021 11:04:41 +0200
Subject: [PATCH] kallisto: update script to match CONTRIBUTING.md
---
src/nf_modules/kallisto/main.nf | 76 +++++----------------------------
1 file changed, 10 insertions(+), 66 deletions(-)
diff --git a/src/nf_modules/kallisto/main.nf b/src/nf_modules/kallisto/main.nf
index 9c85118a..2a9adcbc 100644
--- a/src/nf_modules/kallisto/main.nf
+++ b/src/nf_modules/kallisto/main.nf
@@ -45,79 +45,23 @@ process mapping_fastq {
script:
if (file_id instanceof List){
- pair_id = file_id[0]
+ file_prefix = file_id[0]
} else {
- pair_id = file_id
+ file_prefix = file_id
}
- if (reads instanceof List)
+ if (reads.size() == 2)
"""
- mkdir ${pair_id}
+ mkdir ${file_prefix}
kallisto quant -i ${index} -t ${task.cpus} \
- ${params.mapping_fastq} -o ${pair_id} \
- ${reads[0]} ${reads[1]} &> ${pair_id}_kallisto_mapping_report.txt
+ ${params.mapping_fastq} -o ${file_prefix} \
+ ${reads[0]} ${reads[1]} &> ${file_prefix}_kallisto_mapping_report.txt
"""
- else
+ else if (reads.size() == 1)
"""
- mkdir ${pair_id}
+ mkdir ${file_prefix}
kallisto quant -i ${index} -t ${task.cpus} --single \
- ${params.mapping_fastq} -o ${pair_id} \
- ${reads} &> ${reads.simpleName}_kallisto_mapping_report.txt
+ ${params.mapping_fastq} -o ${file_prefix} \
+ ${reads} &> ${file_prefix}_kallisto_mapping_report.txt
"""
}
-
-params.mapping_fastq_pairedend = "--bias --bootstrap-samples 100"
-params.mapping_fastq_pairedend_out = ""
-process mapping_fastq_pairedend {
- container = "${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:
- tuple val(index_id), path(index)
- tuple val(pair_id), path(reads)
-
- output:
- tuple val(pair_id), path("${pair_id}"), emit: counts
- tuple val(pair_id), path("*_report.txt"), emit: report
-
- script:
-"""
-mkdir ${pair_id}
-kallisto quant -i ${index} -t ${task.cpus} \
-${params.mapping_fastq_pairedend} -o ${pair_id} \
-${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:
- tuple val(index_id), path(index)
- tuple val(file_id), path(reads)
-
- output:
- tuple val(file_id), path("${pair_id}"), emit: counts
- tuple val(file_id), path("*_report.txt"), emit: report
-
- script:
-"""
-mkdir ${file_id}
-kallisto quant -i ${index} -t ${task.cpus} --single \
-${params.mapping_fastq_singleend} -o ${file_id} \
--l ${params.mean} -s ${params.sd} \
-${reads} &> ${reads.simpleName}_kallisto_mapping_report.txt
-"""
-}
--
GitLab