From 329e23003829425a31bb53e0545bcf5199088621 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 29 Apr 2021 14:38:53 +0200
Subject: [PATCH] flexi_splitter: try to fix bug
---
src/nf_modules/flexi_splitter/main.nf | 4 ++--
src/nf_modules/kb/main.nf | 7 ++++---
2 files changed, 6 insertions(+), 5 deletions(-)
diff --git a/src/nf_modules/flexi_splitter/main.nf b/src/nf_modules/flexi_splitter/main.nf
index 6e01c268..d7a87b94 100644
--- a/src/nf_modules/flexi_splitter/main.nf
+++ b/src/nf_modules/flexi_splitter/main.nf
@@ -30,10 +30,10 @@ process split {
if (reads.size() == 2)
"""
- flexi_splitter ${params.split} -f ${reads[0]} ${reads[1]} -c ${config} -o split
+ flexi_splitter ${params.split} -n 2 -f ${reads[0]} ${reads[1]} -o split -c ${config}
"""
else
"""
- flexi_splitter ${params.split} -f ${reads[0]} -c ${config} -o split
+ flexi_splitter ${params.split} -n 1 -f ${reads[0]} -o split -c ${config}
"""
}
diff --git a/src/nf_modules/kb/main.nf b/src/nf_modules/kb/main.nf
index fe08a0df..0dcc470d 100644
--- a/src/nf_modules/kb/main.nf
+++ b/src/nf_modules/kb/main.nf
@@ -137,6 +137,7 @@ process kb_default {
tuple val(file_id), path("*_report.txt"), emit: report
script:
+ def kb_memory = "${task.memory}" - ~/GB/
if (file_id instanceof List){
file_prefix = file_id[0]
} else {
@@ -151,7 +152,7 @@ process kb_default {
"""
mkdir ${file_prefix}
kb count -t ${task.cpus} \
- -m ${task.memory} \
+ -m ${kb_memory} \
-i ${index} \
-g ${transcript_to_gene} \
${whitelist_param} \
@@ -185,7 +186,7 @@ process kb_marseq {
tuple val(file_id), path("*_report.txt"), emit: report
script:
- memory = "${task.memory}" - ~/\s*GB/
+ def kb_memory = "${task.memory}" - ~/GB/
if (file_id instanceof List){
file_prefix = file_id[0]
} else {
@@ -200,7 +201,7 @@ process kb_marseq {
"""
mkdir ${file_prefix}
kb count -t ${task.cpus} \
- -m ${memory} \
+ -m ${kb_memory} \
-i ${index} \
-g ${transcript_to_gene} \
${whitelist_param} \
--
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