From e5a500dacf6b7c47a6e2d4641601ffba316881c4 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 3 May 2021 11:06:14 +0200
Subject: [PATCH] flexi_splitter: reformat output file to avoid file name
conflict
---
src/nf_modules/flexi_splitter/main.nf | 37 ++++++++++++++++++++++++---
1 file changed, 34 insertions(+), 3 deletions(-)
diff --git a/src/nf_modules/flexi_splitter/main.nf b/src/nf_modules/flexi_splitter/main.nf
index 42d405af..c1b82af1 100644
--- a/src/nf_modules/flexi_splitter/main.nf
+++ b/src/nf_modules/flexi_splitter/main.nf
@@ -4,11 +4,26 @@ container_url = "lbmc/flexi_splitter:${version}"
params.split = ""
params.split_out = ""
-process split {
+
+workflow split {
+ take:
+ reads
+ config
+ main:
+ split_file(reads, config)
+ split_file.out.fastq.view()
+
+
+
+ emit:
+ fastq = split_file.out.fastq
+}
+
+process split_file {
// You can get an example of config file here:
// src/nf_modules/flexi_splitter/marseq_flexi_splitter.yaml
container = "${container_url}"
- label "big_mem_multi_cpus"
+ label "big_mem_mono_cpus"
tag "$file_prefix"
if (params.split_out != "") {
publishDir "results/${params.split_out}", mode: 'copy'
@@ -19,7 +34,7 @@ process split {
tuple val(config_id), path(config)
output:
- tuple val(file_id), path("*"), emit: fastq
+ tuple val(file_id), path("split/*/*"), emit: fastq
script:
if (file_id instanceof List){
@@ -31,9 +46,25 @@ process split {
if (reads.size() == 2)
"""
flexi_splitter ${params.split} -n 2 -f ${reads[0]},${reads[1]} -o split -c ${config}
+ rm -Rf split/unassigned
+ find split -type "f" | \
+ sed -E "s|(.*/split/(.*)/(.*))|\1 \2_\3|g" |
+ awk '{"mv "\$1" "\$2"}'
+ rm -Rf split
+ mkdir -p results/
+ find split -type "f" | \
+ sed -E "s|(.*/split/(.*)/(.*))|\1 \2_\3|g" |
+ awk '{"mv "\$1" results/"\$2"}'
+ rm -Rf split
"""
else
"""
flexi_splitter ${params.split} -n 1 -f ${reads[0]} -o split -c ${config}
+ rm -Rf split/unassigned
+ mkdir -p results/
+ find split -type "f" | \
+ sed -E "s|(.*/split/(.*)/(.*))|\1 \2_\3|g" |
+ awk '{"mv "\$1" results/"\$2"}'
+ rm -Rf split
"""
}
--
GitLab