From 6a3f73f5515ab3f0068e008be0e39e851b32b23a Mon Sep 17 00:00:00 2001
From: xgrand <xavier.grand@inserm.fr>
Date: Wed, 31 May 2023 17:06:20 +0200
Subject: [PATCH] Modif arriba_fusion.nf to complete with fusion_parser module.
---
clean.sh | 2 ++
src/arriba_fusion.nf | 4 ++--
2 files changed, 4 insertions(+), 2 deletions(-)
create mode 100755 clean.sh
diff --git a/clean.sh b/clean.sh
new file mode 100755
index 0000000..da5f9a7
--- /dev/null
+++ b/clean.sh
@@ -0,0 +1,2 @@
+rm -f .nextflow.log*
+rm -rf work/*
diff --git a/src/arriba_fusion.nf b/src/arriba_fusion.nf
index f183a87..7a33655 100644
--- a/src/arriba_fusion.nf
+++ b/src/arriba_fusion.nf
@@ -70,7 +70,7 @@ if (params.help || params.h) {
****************************************************************
*/
-params.fastq = "./data/fastq/*_{1,2}.fq*"
+params.fastq = "./data/fastq/*_R{1,2}.fastq.gz"
params.bam = ""
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"
@@ -242,5 +242,5 @@ workflow {
*/
concat_fusion(arriba.out.fusions, arriba.out.discarded)
- parsefusion(concat_fusion.out.concatenated_fusions)
+ parsefusion(concat_fusion.out.concatenated_fusions, htseq_count.out.counts, design.collect())
}
\ No newline at end of file
--
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