From 04fa21c5b9127f38a7b54c8e8ddb9559466a22f4 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 17 Feb 2021 10:56:48 +0100
Subject: [PATCH] nextflow.config: change errorStrategy
---
src/nextflow.config | 6 ++++++
1 file changed, 6 insertions(+)
diff --git a/src/nextflow.config b/src/nextflow.config
index 925ec23c..c1afd1e2 100644
--- a/src/nextflow.config
+++ b/src/nextflow.config
@@ -17,6 +17,7 @@ profiles {
docker.temp = "auto"
docker.enabled = true
process {
+ errorStrategy 'finish'
memory = '16 GB'
withLabel: big_mem_mono_cpus {
cpus = 1
@@ -30,6 +31,7 @@ profiles {
singularity.enabled = true
singularity.cacheDir = "./bin/"
process {
+ errorStrategy 'finish'
memory = '16 GB'
withLabel: big_mem_mono_cpus {
cpus = 1
@@ -44,6 +46,8 @@ profiles {
singularity.cacheDir = "$baseDir/.singularity_psmn/"
singularity.runOptions = "--bind /Xnfs,/scratch"
process{
+ errorStrategy { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' }
+ maxRetries 3
withLabel: big_mem_mono_cpus {
executor = "sge"
clusterOptions = "-cwd -V"
@@ -70,6 +74,8 @@ profiles {
singularity.cacheDir = "$baseDir/.singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
+ errorStrategy { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' }
+ maxRetries 3
withLabel: big_mem_mono_cpus {
scratch = true
stageInMode = "copy"
--
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