diff --git a/snappy_pipeline/workflows/varfish_export/__init__.py b/snappy_pipeline/workflows/varfish_export/__init__.py index b48e0a239..f4c07d0d5 100644 --- 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 index 9400d560e..dce342909 100644 --- 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} < {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 index d36788a17..7ea72deac 100644 --- 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} < {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 index fec4b885e..065eca483 100644 --- 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