From 89474c571c36c1eec4f660f66b613712181e4c70 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 22 Jul 2024 11:49:22 +0200
Subject: [PATCH] parasplit: fix parameters duplication
---
conf/modules.config | 4 ++--
modules/local/parasplit.nf | 2 +-
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/conf/modules.config b/conf/modules.config
index 1d85bb1..bdfe70c 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -471,8 +471,8 @@ process {
}
withName: 'PARASPLIT' {
- ext.output_for = { "${meta1.id}_${meta1.chunk}_${meta1.mates}_digested.fastq" }
- ext.output_rev = { "${meta2.id}_${meta2.chunk}_${meta2.mates}_digested.fastq" }
+ ext.output_for = { "${meta1.id}_${meta1.chunk}_${meta1.mates}_digested.fastq.gz" }
+ ext.output_rev = { "${meta2.id}_${meta2.chunk}_${meta2.mates}_digested.fastq.gz" }
ext.args = { [
" --mode ${params.parasplit_mode}",
" --seed_size ${params.parasplit_seed}"
diff --git a/modules/local/parasplit.nf b/modules/local/parasplit.nf
index f969900..f0c978a 100644
--- a/modules/local/parasplit.nf
+++ b/modules/local/parasplit.nf
@@ -18,7 +18,7 @@ process PARASPLIT {
def output_rev = task.ext.output_rev ?: "${meta2.id}_${meta2.chunk}_${meta2.mates}.fastq.gz"
"""
- parasplit -sf ${reads1} -sr ${reads2} -le ${digestion} -of ${output_for} -or ${output_rev} -nt ${task.cpus} -sz 20 -m all ${args}
+ parasplit -sf ${reads1} -sr ${reads2} -le ${digestion} -of ${output_for} -or ${output_rev} -nt ${task.cpus} ${args}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
parasplit: \$(parasplit --version)
--
GitLab