From a7f5de2bd9e741cef79fe386fe6af4cfa0fba443 Mon Sep 17 00:00:00 2001
From: Xavier Grand <157-xgrand@users.noreply.gitbio.ens-lyon.fr>
Date: Wed, 27 Jul 2022 09:17:44 +0200
Subject: [PATCH] RNAseq_XGR, modif star:main_2.7.8a.nf input index val
---
src/nf_modules/star/main_2.7.8a.nf | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/src/nf_modules/star/main_2.7.8a.nf b/src/nf_modules/star/main_2.7.8a.nf
index b544b2f..e7be9f7 100644
--- a/src/nf_modules/star/main_2.7.8a.nf
+++ b/src/nf_modules/star/main_2.7.8a.nf
@@ -211,7 +211,7 @@ if (reads_id instanceof List){
if (reads.size() == 2)
"""
STAR --runThreadN ${task.cpus} \
---genomeDir $index \
+--genomeDir ${index} \
--readFilesCommand zcat \
--readFilesIn ${reads[0]} ${reads[1]} \
--outFileNamePrefix ${reads_id}. \
@@ -224,7 +224,7 @@ mv ${reads_id}.Aligned.sortedByCoord.out.bam ${reads_id}.bam
else
"""
STAR --runThreadN ${task.cpus} \
---genomeDir $index \
+--genomeDir ${index} \
--readFilesCommand zcat \
--readFilesIn ${reads} \
--outFileNamePrefix ${reads_id}. \
--
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