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bihealth · Apr 11, 2023 · 7ee1428 · 7ee1428
1 parent 94b1d88
commit 7ee1428
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Showing 3 changed files with 11 additions and 4 deletions.
diff --git a/snappy_pipeline/workflows/variant_annotation/Snakefile b/snappy_pipeline/workflows/variant_annotation/Snakefile
@@ -39,7 +39,7 @@ rule all:
 
 rule variant_annotation_vep_run:
     input:
-        unpack(wf.get_input_files("vep", "run")),
+        **wf.get_input_files("vep", "run"),
     output:
         **wf.get_output_files("vep", "run"),
     threads: wf.get_resource("vep", "run", "threads")

diff --git a/snappy_pipeline/workflows/variant_annotation/__init__.py b/snappy_pipeline/workflows/variant_annotation/__init__.py
@@ -100,6 +100,8 @@
       num_threads: 16
       # Additional flags.
       more_flags: "--af_gnomade --af_gnomadg"
+      # The --buffer_size parameter
+      buffer_size: 100000
 """
 
 

diff --git a/snappy_wrappers/wrappers/vep/wrapper.py b/snappy_wrappers/wrappers/vep/wrapper.py
@@ -54,9 +54,9 @@
 
 vep --verbose \
     --fasta {snakemake.config[static_data_config][reference][path]} \
-    --input_file {snakemake.input} \
-    --output_file {snakemake.output} \
-    --format vcf \
+    --input_file {snakemake.input.vcf} \
+    --output_file {snakemake.output.vcf} \
+    --compress_output bgzip \
     --vcf \
     --symbol \
     --terms SO \
@@ -65,6 +65,7 @@
     --offline \
     --{snakemake.config[step_config][variant_annotation][vep][tx_flag]} \
     --force_overwrite \
+    --buffer_size {snakemake.config[step_config][variant_annotation][vep][buffer_size]} \
     $(if [[ ! -z "{snakemake.config[step_config][variant_annotation][vep][cache_dir]}" ]]; then \
         echo --dir_cache {snakemake.config[step_config][variant_annotation][vep][cache_dir]}; \
     fi) \
@@ -73,6 +74,10 @@
     --fork {snakemake.config[step_config][variant_annotation][vep][num_threads]} \
     {snakemake.config[step_config][variant_annotation][vep][more_flags]}
 
+tabix -f {snakemake.output.vcf}
+compute-md5 {snakemake.output.vcf} {snakemake.output.vcf_md5}
+compute-md5 {snakemake.output.vcf_tbi} {snakemake.output.vcf_tbi_md5}
+
 # Create output links -----------------------------------------------------------------------------
 
 for path in {snakemake.output.output_links}; do