From f4e08eb8a0b22a10e1c8555f83ea4bf8e52aa4fc Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 10 Mar 2021 17:13:36 +0100
Subject: [PATCH] gatk4: switch PrintRead to ApplyBQSR
---
src/nf_modules/gatk4/main.nf | 6 ++----
1 file changed, 2 insertions(+), 4 deletions(-)
diff --git a/src/nf_modules/gatk4/main.nf b/src/nf_modules/gatk4/main.nf
index 82526e7f..c767ed70 100644
--- a/src/nf_modules/gatk4/main.nf
+++ b/src/nf_modules/gatk4/main.nf
@@ -152,12 +152,10 @@ process recalibrate_snp {
script:
xmx_memory = "${task.memory}" - ~/\s*GB/
"""
-gatk --java-options "-Xmx${xmx_memory}G" PrintReads \
- --use_jdk_deflater \
- --use_jdk_inflater \
+gatk --java-options "-Xmx${xmx_memory}G" ApplyBQSR \
-R ${fasta} \
-I ${bam} \
- -BQSR recal_data_table \
+ --bqsr-recal-file recal_data_table \
-O ${file_id}_recal.bam
"""
}
--
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