From d233ceef96540fa61d2b25b566522fe3c646642c Mon Sep 17 00:00:00 2001
From: xgrand <xavier.grand@inserm.fr>
Date: Wed, 17 May 2023 16:15:49 +0200
Subject: [PATCH] modif arriba_fusion.nf, still in progress
---
src/arriba_fusion.nf | 8 ++++----
src/nextflow.config | 6 +++---
2 files changed, 7 insertions(+), 7 deletions(-)
diff --git a/src/arriba_fusion.nf b/src/arriba_fusion.nf
index ea200ac..52b2f5c 100644
--- a/src/arriba_fusion.nf
+++ b/src/arriba_fusion.nf
@@ -69,11 +69,11 @@ if (params.help || params.h) {
****************************************************************
*/
-params.fastq = ""
+params.fastq = "./data/fastq/*_{1,2}.fq*"
params.bam = ""
-params.genome = ""
-params.gtf = ""
-params.index = ""
+params.genome = "/home/xavier/Data/Genome/hg19/Homo_sapiens.GRCh37.dna.primary_assembly.fa"
+params.gtf = "/home/xavier/Data/Genome/hg19/Homo_sapiens.GRCh37.87.gtf"
+params.index = "/home/xavier/Data/Genome/hg19/STAR"
/* Params out */
params.fastp_out = "02_fastp"
diff --git a/src/nextflow.config b/src/nextflow.config
index 29f2a25..7e61f1f 100644
--- a/src/nextflow.config
+++ b/src/nextflow.config
@@ -83,14 +83,14 @@ profiles {
cpus = 1
}
withLabel: big_mem_multi_cpus {
- cpus = 8
+ cpus = 4
}
withLabel: small_mem_mono_cpus {
cpus = 1
memory = '2GB'
}
withLabel: small_mem_multi_cpus {
- cpus = 8
+ cpus = 4
memory = '2GB'
}
withLabel: mid_mem_mono_cpus {
@@ -98,7 +98,7 @@ profiles {
memory = '8GB'
}
withLabel: mid_mem_multi_cpus {
- cpus = 8
+ cpus = 4
memory = '8GB'
}
}
--
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