From b065fac0d2fa043d41b06a7b119b5df171ba25c6 Mon Sep 17 00:00:00 2001
From: cbedet1 <cecile.bedet@ens-lyon.fr>
Date: Thu, 24 Mar 2022 09:56:33 +0100
Subject: [PATCH] change -s option for no for RNAseq analysis of Andrea fatsq
(project Strome with Valerie)
---
src/nf_modules/htseq/main.nf | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/nf_modules/htseq/main.nf b/src/nf_modules/htseq/main.nf
index e7fb52d..723c8b8 100644
--- a/src/nf_modules/htseq/main.nf
+++ b/src/nf_modules/htseq/main.nf
@@ -36,7 +36,7 @@ process htseq_count {
script:
"""
-htseq-count -n ${task.cpus} -r pos -a 10 -s reverse -t exon -i gene_id $bam $gtf_file > ${file_id}.tsv
+htseq-count -n ${task.cpus} -r pos -a 10 -s no -t exon -i gene_id $bam $gtf_file > ${file_id}.tsv
"""
}
--
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