docker file for deepvariant added

IntelLabs · Sep 4, 2024 · 74c754d · 74c754d
1 parent c8a81d6
commit 74c754d
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Showing 2 changed files with 11 additions and 4 deletions.
diff --git a/pipelines/deepvariant-based-germline-variant-calling-fq2vcf/config b/pipelines/deepvariant-based-germline-variant-calling-fq2vcf/config
@@ -0,0 +1,7 @@
+export LD_PRELOAD=/Open-Omics-Acceleration-Framework/pipelines/deepvariant-based-germline-variant-calling-fq2vcf/libmimalloc.so.2.0:$LD_PRELOAD
+export INPUT_DIR=/reads/
+export OUTPUT_DIR=/output/
+export REF_DIR=/ref/
+REF=GCA_000001405.15_GRCh38_no_alt_analysis_set.fna
+R1=HG001_R1.fastq.gz
+R2=HG001_R2.fastq.gz
diff --git a/pipelines/deepvariant-based-germline-variant-calling-fq2vcf/extra_scripts/config b/pipelines/deepvariant-based-germline-variant-calling-fq2vcf/extra_scripts/config
@@ -1,4 +1,4 @@
-export INPUT_DIR=/output_dir/ 
-export OUTPUT_DIR=/output_dir/
-export REF_DIR=/data/
-REF=GCA_000001405.15_GRCh38_no_alt_analysis_set.fna
+export INPUT_DIR=/output/ 
+export OUTPUT_DIR=/output/
+export REF_DIR=/ref/
+export REF=GCA_000001405.15_GRCh38_no_alt_analysis_set.fna