Merge pull request #42 from molgenis/feat/cadd-perf

Fix #38 Skip precomputed CADD scores for CAPICE
molgenis · Sep 15, 2020 · a4086eb · a4086eb
2 parents 2f39b9f + e780a03
commit a4086eb
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/pipeline_annotate.sh b/pipeline_annotate.sh
@@ -222,7 +222,7 @@ 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