Change name of directory to 'variant-annotations-table'

broadinstitute · Sep 10, 2024 · 460fe70 · 460fe70
1 parent 0ff7491
commit 460fe70
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Showing 11 changed files with 7 additions and 7 deletions.
diff --git a/.dockstore.yml b/.dockstore.yml
@@ -200,7 +200,7 @@ workflows:
              - /.*/
    - name: GvsCreateVATfromVDS
      subclass: WDL
-     primaryDescriptorPath: /scripts/variantstore/wdl/variant_annotation_table/GvsCreateVATfromVDS.wdl
+     primaryDescriptorPath: /scripts/variantstore/wdl/variant-annotations-table/GvsCreateVATfromVDS.wdl
      filters:
          branches:
              - master
@@ -209,7 +209,7 @@ workflows:
              - /.*/
    - name: GvsCreateVATFilesFromBigQuery
      subclass: WDL
-     primaryDescriptorPath: /scripts/variantstore/variant_annotations_table/GvsCreateVATFilesFromBigQuery.wdl
+     primaryDescriptorPath: /scripts/variantstore/variant-annotations-table/GvsCreateVATFilesFromBigQuery.wdl
      filters:
          branches:
              - master
@@ -218,9 +218,9 @@ workflows:
              - /.*/
    - name: GvsValidateVat
      subclass: WDL
-     primaryDescriptorPath: /scripts/variantstore/variant_annotations_table/GvsValidateVAT.wdl
+     primaryDescriptorPath: /scripts/variantstore/variant-annotations-table/GvsValidateVAT.wdl
      testParameterFiles:
-         - /scripts/variantstore/variant_annotations_table/GvsValidateVat.example.inputs.json
+         - /scripts/variantstore/variant-annotations-table/GvsValidateVat.example.inputs.json
      filters:
          branches:
              - master

diff --git a/scripts/variantstore/docs/aou/AOU_DELIVERABLES.md b/scripts/variantstore/docs/aou/AOU_DELIVERABLES.md
@@ -98,7 +98,7 @@ The Callset Stats and S&P files can be simply `gsutil cp`ed to the AoU delivery
 
 ## Running the VAT pipeline
 To create a BigQuery table of variant annotations, you may follow the instructions here:
-[process to create variant annotations table](../../variant_annotations_table/README.md)
+[process to create variant annotations table](../../variant-annotations-table/README.md)
 
 The pipeline takes in the VDS and outputs a variant annotations table in BigQuery.
 

diff --git a/...tore/variant_annotations_table/Dockerfile → ...tore/variant-annotations-table/Dockerfile b/...tore/variant_annotations_table/Dockerfile → ...tore/variant-annotations-table/Dockerfile
diff --git a/...s_table/GvsCreateVATFilesFromBigQuery.wdl → ...s-table/GvsCreateVATFilesFromBigQuery.wdl b/...s_table/GvsCreateVATFilesFromBigQuery.wdl → ...s-table/GvsCreateVATFilesFromBigQuery.wdl
diff --git a/...annotations_table/GvsCreateVATfromVDS.wdl → ...annotations-table/GvsCreateVATfromVDS.wdl b/...annotations_table/GvsCreateVATfromVDS.wdl → ...annotations-table/GvsCreateVATfromVDS.wdl
diff --git a/..._table/GvsValidateVAT.example.inputs.json → ...-table/GvsValidateVAT.example.inputs.json b/..._table/GvsValidateVAT.example.inputs.json → ...-table/GvsValidateVAT.example.inputs.json
diff --git a/...iant_annotations_table/GvsValidateVAT.wdl → ...iant-annotations-table/GvsValidateVAT.wdl b/...iant_annotations_table/GvsValidateVAT.wdl → ...iant-annotations-table/GvsValidateVAT.wdl
diff --git a/...store/variant_annotations_table/README.md → ...store/variant-annotations-table/README.md b/...store/variant_annotations_table/README.md → ...store/variant-annotations-table/README.md
@@ -5,8 +5,8 @@ The pipeline takes in a Hail Variant Dataset (VDS), creates a queryable table in
 
 ### VAT WDLs
 
-- [GvsCreateVATfromVDS.wdl](/scripts/variantstore/variant_annotations_table/GvsCreateVATfromVDS.wdl) creates a sites only VCF from a VDS and then uses that and an ancestry file TSV to build the variant annotations table.
-- [GvsValidateVAT.wdl](/scripts/variantstore/variant_annotations_table/GvsValidateVAT.wdl) checks and validates the created VAT and prints a report of any failing validation.
+- [GvsCreateVATfromVDS.wdl](/scripts/variantstore/variant-annotations-table/GvsCreateVATfromVDS.wdl) creates a sites only VCF from a VDS and then uses that and an ancestry file TSV to build the variant annotations table.
+- [GvsValidateVAT.wdl](/scripts/variantstore/variant-annotations-table/GvsValidateVAT.wdl) checks and validates the created VAT and prints a report of any failing validation.
 
 ### Run GvsCreateVATfromVDS
 

diff --git a/...ons_table/Reference Disk Terra Opt In.png → ...ons-table/Reference Disk Terra Opt In.png b/...ons_table/Reference Disk Terra Opt In.png → ...ons-table/Reference Disk Terra Opt In.png
diff --git a/...variant_annotations_table/build_docker.sh → ...variant-annotations-table/build_docker.sh b/...variant_annotations_table/build_docker.sh → ...variant-annotations-table/build_docker.sh
diff --git a/...ons_table/custom_annotations_template.tsv → ...ons-table/custom_annotations_template.tsv b/...ons_table/custom_annotations_template.tsv → ...ons-table/custom_annotations_template.tsv