From 00d80ce7c4b5dc4d4e732939ef8487da11a6fa1a Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 8 Jun 2023 14:19:16 +0200
Subject: [PATCH] add projectDir for kmerclust
---
src/modules/kmerclust.nf | 2 +-
src/nextflow.config | 4 ++--
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/src/modules/kmerclust.nf b/src/modules/kmerclust.nf
index 3f652da..74a5fbf 100644
--- a/src/modules/kmerclust.nf
+++ b/src/modules/kmerclust.nf
@@ -16,7 +16,7 @@ process KMERCLUST {
script:
def args = task.ext.args ?: ''
"""
- Rscript ../bin/kmerclust.R ${params.csv} ${csv} ${specie} ${task.cpus}
+ Rscript ${projectDir}/bin/kmerclust.R ${params.csv} ${csv} ${specie} ${task.cpus}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
diff --git a/src/nextflow.config b/src/nextflow.config
index 76baf88..58daa85 100644
--- a/src/nextflow.config
+++ b/src/nextflow.config
@@ -20,8 +20,8 @@ profiles {
charliecloud.runOptions = "--bind /scratch:/scratch --bind /Xnfs:/Xnfs --bind /home:/home"
process{
- errorStrategy = { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' }
- maxRetries = 3
+ //errorStrategy = { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' }
+ //maxRetries = 3
executor = "slurm"
queue = "Lake"
withLabel: big_mem_mono_cpus {
--
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