From 5fd3ab953d76a7c89757fb9d60b423fdd06c7292 Mon Sep 17 00:00:00 2001
From: william <william.desaintjean@ens-lyon.fr>
Date: Fri, 16 Feb 2024 10:04:27 +0100
Subject: [PATCH] =?UTF-8?q?pas=20d'index=20par=20d=C3=A9faut?=
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---
src/arriba_fusion.nf | 4 +++-
src/nextflow.config | 7 +++++++
src/nf_modules/star/main_2.7.8a.nf | 2 +-
3 files changed, 11 insertions(+), 2 deletions(-)
diff --git a/src/arriba_fusion.nf b/src/arriba_fusion.nf
index 474e580..dc648e1 100644
--- a/src/arriba_fusion.nf
+++ b/src/arriba_fusion.nf
@@ -77,9 +77,11 @@ params.design = ""
params.genome = "/home/xavier/Data/Genome/hg19/Homo_sapiens.GRCh37.dna.primary_assembly.fa"
params.cyto = "/home/xavier/Programs/arriba_v2.3.0/database/cytobands_hg19_hs37d5_GRCh37_v2.3.0.tsv"
params.gtf = "/home/xavier/Data/Genome/hg19/Homo_sapiens.GRCh37.87.gtf"
-params.index = "/home/xavier/Data/Genome/hg19/STAR"
+//params.index = "/home/xavier/Data/Genome/hg19/STAR"
+params.index = ""
params.htseq_param = "yes"
+
/* Specific Arriba parameters */
params.arriba_options = "-f 'blacklist,read_through' \
-E 1 \
diff --git a/src/nextflow.config b/src/nextflow.config
index ed18089..b4c1642 100644
--- a/src/nextflow.config
+++ b/src/nextflow.config
@@ -125,6 +125,13 @@ profiles {
time = "24h"
clusterOptions = "--partition=Lake"
}
+ withLabel: ultra_mem_multi_cpus {
+ executor = "slurm"
+ cpus = 32
+ memory = "300GB"
+ time = "24h"
+ clusterOptions = "--partition=Lake"
+ }
withLabel: small_mem_mono_cpus {
executor = "slurm"
cpus = 1
diff --git a/src/nf_modules/star/main_2.7.8a.nf b/src/nf_modules/star/main_2.7.8a.nf
index 8f5bd25..26f5d6a 100644
--- a/src/nf_modules/star/main_2.7.8a.nf
+++ b/src/nf_modules/star/main_2.7.8a.nf
@@ -238,7 +238,7 @@ mv ${reads_id}.Aligned.sortedByCoord.out.bam ${reads_id}.bam
process mapping2fusion {
container = "${container_url}"
- label "big_mem_multi_cpus"
+ label "ultra_mem_multi_cpus"
tag "$reads_id"
if (params.star_mapping2fusion_out != "") {
publishDir "results/${params.star_mapping2fusion_out}", mode: 'copy'
--
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