From de91c5959e9acfa77c74d26558ff2c93acc8f1f6 Mon Sep 17 00:00:00 2001 From: Emilio Palumbo 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' } }