From de91c5959e9acfa77c74d26558ff2c93acc8f1f6 Mon Sep 17 00:00:00 2001
From: Emilio Palumbo <emiliopalumbo@gmail.com>
Date: Mon, 17 Jun 2024 13:54:49 +0200
Subject: [PATCH] Update gtex profile
---
nextflow.config | 12 +++++-------
1 file changed, 5 insertions(+), 7 deletions(-)
diff --git a/nextflow.config b/nextflow.config
index 618a675..86ed900 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -180,8 +180,8 @@ profiles {
gtex {
params.fastaIndexTool = "samtools"
params.mappingTool = "STAR"
- params.sortBamTool = "sambamba"
- params.mergeBamTool = "sambamba"
+ params.sortBamTool = "samtools"
+ params.mergeBamTool = "samtools"
params.markdupTool = "sambamba"
params.inferExpTool = "RSeQC"
params.bamStatsTool = "bamstats"
@@ -189,10 +189,8 @@ profiles {
params.contigTool = "RGCRG"
params.quantificationTool = "RSEM"
- params.starVersion = 'v2.5.3a'
- params.rsemVersion = '1.3.0'
-
- params.annotation = "https://storage.googleapis.com/gtex-resources/GENCODE/gencode.v26.GRCh38.genes.collapsed_only.gtf"
- params.genome = "https://storage.googleapis.com/gtex-resources/references/Homo_sapiens_assembly38_noALT_noHLA_noDecoy_ERCC.fasta"
+ params.starVersion = '2.5.3a--0'
+ params.rsemVersion = '1.3.0--pl526r341h4f16992_4'
+ params.samtoolsVersion = '1.6--hc3601fc_10'
}
}