Merge branch 'dev' of github.com:broadinstitute/seqr-loading-pipelines into benb/single_callset_path

Author: bpblanken

v03_pipeline/lib/tasks/__init__.py

@@ -1,3 +1,9 @@
+from v03_pipeline.lib.tasks.delete_family_table import DeleteFamilyTableTask
+from v03_pipeline.lib.tasks.delete_family_tables import DeleteFamilyTablesTask
+from v03_pipeline.lib.tasks.delete_project_family_tables import (
+    DeleteProjectFamilyTablesTask,
+)
+from v03_pipeline.lib.tasks.delete_project_table import DeleteProjectTableTask
 from v03_pipeline.lib.tasks.reference_data.update_cached_reference_dataset_queries import (
     UpdateCachedReferenceDatasetQueries,
 )
@@ -11,6 +17,9 @@
     UpdateLookupTableWithDeletedProjectTask,
 )
 from v03_pipeline.lib.tasks.update_project_table import UpdateProjectTableTask
+from v03_pipeline.lib.tasks.update_project_table_with_deleted_families import (
+    UpdateProjectTableWithDeletedFamiliesTask,
+)
 from v03_pipeline.lib.tasks.update_variant_annotations_table_with_deleted_families import (
     UpdateVariantAnnotationsTableWithDeletedFamiliesTask,
 )
@@ -26,7 +35,12 @@
 )
 
 __all__ = [
+    'DeleteFamilyTableTask',
+    'DeleteFamilyTablesTask',
+    'DeleteProjectFamilyTablesTask',
+    'DeleteProjectTableTask',
     'UpdateProjectTableTask',
+    'UpdateProjectTableWithDeletedFamiliesTask',
     'UpdateLookupTableTask',
     'UpdateLookupTableWithDeletedProjectTask',
     'UpdateLookupTableWithDeletedFamiliesTask',

v03_pipeline/var/vep_config/vep-GRCh38.json

@@ -2,7 +2,7 @@
   "command": [
     "bash",
     "-c",
-    "/vep --format vcf -json --hgvs --biotype --canonical --mane --minimal --numbers --regulatory --allele_number --no_stats --cache --offline --assembly GRCh38 --fasta /opt/vep/.vep/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz --check_ref --dont_skip --plugin LoF,loftee_path:/plugins,gerp_bigwig:/opt/vep/.vep/gerp_conservation_scores.homo_sapiens.GRCh38.bw,human_ancestor_fa:/opt/vep/.vep/human_ancestor.fa.gz,conservation_file:/opt/vep/.vep/loftee.sql --plugin UTRAnnotator,file=/opt/vep/.vep/uORF_5UTR_GRCh38_PUBLIC.txt --plugin SpliceRegion,Extended --plugin AlphaMissense,file=/opt/vep/.vep/AlphaMissense_hg38.tsv.gz --dir_plugins /plugins -o STDOUT | sed s/5utr/fiveutr/g"
+    "/vep --warning_file STDERR --format vcf -json --hgvs --biotype --canonical --mane --minimal --numbers --regulatory --allele_number --no_stats --cache --offline --assembly GRCh38 --fasta /opt/vep/.vep/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz --check_ref --dont_skip --plugin LoF,loftee_path:/plugins,gerp_bigwig:/opt/vep/.vep/gerp_conservation_scores.homo_sapiens.GRCh38.bw,human_ancestor_fa:/opt/vep/.vep/human_ancestor.fa.gz,conservation_file:/opt/vep/.vep/loftee.sql --plugin UTRAnnotator,file=/opt/vep/.vep/uORF_5UTR_GRCh38_PUBLIC.txt --plugin SpliceRegion,Extended --plugin AlphaMissense,file=/opt/vep/.vep/AlphaMissense_hg38.tsv.gz --dir_plugins /plugins -o STDOUT | sed s/5utr/fiveutr/g"
   ],
   "env": {
     "PERL5LIB": "/plugins"