From e780a03bec39935b3c6f75a538d2968cc8df5eac Mon Sep 17 00:00:00 2001
From: Dennis Hendriksen <d.hendriksen@umcg.nl>
Date: Tue, 8 Sep 2020 09:52:25 +0200
Subject: [PATCH] Fix #38 Skip precomputed CADD scores for CAPICE

---
 pipeline_annotate.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pipeline_annotate.sh b/pipeline_annotate.sh
index ba9db1512..1c690c567 100644
--- a/pipeline_annotate.sh
+++ b/pipeline_annotate.sh
@@ -234,7 +234,7 @@ else
 	# strip headers from input vcf for cadd
 	CADD_INPUT="${CAPICE_OUTPUT_DIR}/input_headerless_$(date +%s).vcf.gz"
 	gunzip -c $CAPICE_INPUT | sed '/^#/d' | bgzip > ${CADD_INPUT}
-	CADD.sh -a -g ${ASSEMBLY} -o ${CAPICE_OUTPUT_DIR}/cadd.tsv.gz ${CADD_INPUT}
+	CADD.sh -a -g ${ASSEMBLY} -o ${CAPICE_OUTPUT_DIR}/cadd.tsv.gz -c ${CPU_CORES} -s ${CADD_INPUT}
 	module purge
 
 	module load CAPICE