Bumping varfish-annotator-cli (#168)

Also, passing in pedigree file to annotator.
bihealth · Aug 28, 2022 · 84c068a · 84c068a
1 parent 7a7b810
commit 84c068a
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diff --git a/snappy_wrappers/wrappers/varfish_annotator/annotate/wrapper.py b/snappy_wrappers/wrappers/varfish_annotator/annotate/wrapper.py
@@ -82,10 +82,12 @@
     \
     --release {export_config[release]} \
     \
+    --self-test-chr1-only \
     --ref-path {snakemake.config[static_data_config][reference][path]} \
     --db-path {export_config[path_db]} \
     --refseq-ser-path {export_config[path_refseq_ser]} \
     --ensembl-ser-path {export_config[path_ensembl_ser]} \
+    --input-ped {snakemake.input.ped} \
     \
     --input-vcf $TMPDIR/tmp.vcf.gz \
     --output-db-info ${{out_db_info%.gz}} \

diff --git a/snappy_wrappers/wrappers/varfish_annotator/annotate_sv/wrapper.py b/snappy_wrappers/wrappers/varfish_annotator/annotate_sv/wrapper.py
@@ -94,6 +94,7 @@
     --db-path {export_config[path_db]} \
     --refseq-ser-path {export_config[path_refseq_ser]} \
     --ensembl-ser-path {export_config[path_ensembl_ser]} \
+    --input-ped {snakemake.input.ped} \
     \
     --input-vcf $TMPDIR/tmp.vcf.gz \
     --output-db-info ${{out_db_info%.gz}} \

diff --git a/snappy_wrappers/wrappers/varfish_annotator/environment.yaml b/snappy_wrappers/wrappers/varfish_annotator/environment.yaml
@@ -4,5 +4,6 @@ channels:
 dependencies:
   - bcftools >=1.9
   - htslib >=1.9
-  - varfish-annotator-cli ==0.21
+  - varfish-annotator-cli ==0.25
+  - openjdk >=8,<9
   - jq