From 1edca65d0dac70f9be1c5e330ae7f9f7694c5f6b Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 10 Mar 2021 11:58:32 +0100
Subject: [PATCH] gatk4: fix BaseRecalibrator params
---
src/nf_modules/gatk4/main.nf | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/src/nf_modules/gatk4/main.nf b/src/nf_modules/gatk4/main.nf
index 82784453..63803f26 100644
--- a/src/nf_modules/gatk4/main.nf
+++ b/src/nf_modules/gatk4/main.nf
@@ -128,8 +128,8 @@ process recalibrate_snp_table {
gatk --java-options "-Xmx${xmx_memory}G" BaseRecalibrator \
-R ${fasta} \
-I ${bam} \
- -knownSites ${snp_file} \
- -knownSites ${indel_file} \
+ -known-sites ${snp_file} \
+ -known-sites ${indel_file} \
-O recal_data_table
"""
}
--
GitLab