From 4a34c96bad6b4559f022e99d48786b7c0031c59f Mon Sep 17 00:00:00 2001
From: Xavier Grand <xavier.grand@ens-lyon.fr>
Date: Tue, 26 Jul 2022 14:18:28 +0200
Subject: [PATCH] Modif RNAseq_XGR.nf to use STAR indexed genome
---
src/RNAseq_XGR.nf | 2 +-
src/nf_modules/star/main_2.7.8a.nf | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/src/RNAseq_XGR.nf b/src/RNAseq_XGR.nf
index 3241542..2dc6169 100644
--- a/src/RNAseq_XGR.nf
+++ b/src/RNAseq_XGR.nf
@@ -31,8 +31,8 @@ def helpMessage() {
References:
--fasta [path] Path to genome fasta file.
- --genome [path] Path to STAR indexed genome. (To avoid the time consumming indexation of "STAR genome generate" step)
--gtf [path] Path to the gtf annotation file.
+ --idx [path] Path to the STAR indexed genome (optional). (If allready computed)
Help: Display this help message.
--help
diff --git a/src/nf_modules/star/main_2.7.8a.nf b/src/nf_modules/star/main_2.7.8a.nf
index 159e139..7ee0ac3 100644
--- a/src/nf_modules/star/main_2.7.8a.nf
+++ b/src/nf_modules/star/main_2.7.8a.nf
@@ -194,7 +194,7 @@ process mapping_withindex {
}
input:
- tuple val(index_id), path(index)
+ path(index)
tuple val(reads_id), path(reads)
output:
--
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