make work in practice

bihealth · May 2, 2023 · db04420 · db04420
1 parent e6d3b10
commit db04420
Show file tree

Hide file tree

Showing 4 changed files with 4 additions and 13 deletions.
diff --git a/snappy_pipeline/workflows/varfish_export/__init__.py b/snappy_pipeline/workflows/varfish_export/__init__.py
@@ -391,8 +391,6 @@ def _get_output_files_annotate_strucvars(self):
         work_paths = {
             "gts": f"{prefix}.gts.tsv.gz",
             "gts_md5": f"{prefix}.gts.tsv.gz.md5",
-            "feature_effects": f"{prefix}.feature-effects.tsv.gz",
-            "feature_effects_md5": f"{prefix}.feature-effects.tsv.gz.md5",
             "db_infos": f"{prefix}.db-infos.tsv.gz",
             "db_infos_md5": f"{prefix}.db-infos.tsv.gz.md5",
         }

diff --git a/snappy_wrappers/wrappers/mehari/annotate_seqvars/wrapper.py b/snappy_wrappers/wrappers/mehari/annotate_seqvars/wrapper.py
@@ -75,19 +75,16 @@
     ln -sr {snakemake.input.vcf}.tbi $TMPDIR/tmp.vcf.gz.tbi
 fi
 
-release=$(echo {export_config[release]} | tr '[:upper:]' '[:lower:]')
-
 # Perform Mehari sequence variant annotation.
 mehari \
     annotate \
     seqvars \
-    --release ${release} \
     --path-db {export_config[path_mehari_db]} \
     --path-input-ped {snakemake.input.ped} \
     --path-input-vcf $TMPDIR/tmp.vcf.gz \
-    --path-output-tsv >(gzip -c > {snakemake.output.gts})
+    --path-output-tsv {snakemake.output.gts}
 
-cat | gzip -c > {snakemake.output.db-infos} <<EOF
+cat <<EOF | gzip -c > {snakemake.output.db_infos}
 genomebuild	db_name	release
 GRCh37	clinvar	20210728
 GRCh37	gnomad_exomes	r2.1.1

diff --git a/snappy_wrappers/wrappers/mehari/annotate_strucvars/wrapper.py b/snappy_wrappers/wrappers/mehari/annotate_strucvars/wrapper.py
@@ -103,20 +103,16 @@
     done) \
     --path-output-tsv >(gzip -c > {snakemake.output.gts})
 
-cat | gzip -c > {snakemake.output.db-infos} <<EOF
+cat <<EOF | gzip -c > {snakemake.output.db_infos}
 genomebuild	db_name	release
 GRCh37	clinvar	20210728
 GRCh37	gnomad_exomes	r2.1.1
 GRCh37	gnomad_genomes	r2.1.1
 EOF
 
-# Copy out PED file to output
-cp -H {snakemake.input.ped} {snakemake.output.ped}
-
 # Compute MD5 sums on output files
 compute-md5 {snakemake.output.db_infos} {snakemake.output.db_infos_md5}
 compute-md5 {snakemake.output.gts} {snakemake.output.gts_md5}
-compute-md5 {snakemake.output.feature_effects} {snakemake.output.feature_effects_md5}
 
 # Create output links -----------------------------------------------------------------------------
 

diff --git a/snappy_wrappers/wrappers/mehari/environment.yaml b/snappy_wrappers/wrappers/mehari/environment.yaml
@@ -5,7 +5,7 @@ dependencies:
   - bcftools >=1.9
   - htslib >=1.9
   - samtools >=1.9
-  - mehari ==0.2.0
+  - mehari ==0.2.1
   - jq
   - vcfpy
   - pysam