Gg vs 1990 a widdle cleanup (#8970)

* Moving some wdls around. * Remove HailFromWdl.wdl
broadinstitute · Sep 27, 2024 · 4966cff · 4966cff
1 parent 213366d
commit 4966cff
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Showing 21 changed files with 31 additions and 286 deletions.
diff --git a/.dockstore.yml b/.dockstore.yml
@@ -101,7 +101,7 @@ workflows:
              - /.*/
    - name: GvsBenchmarkExtractTask
      subclass: WDL
-     primaryDescriptorPath: /scripts/variantstore/wdl/GvsBenchmarkExtractTask.wdl
+     primaryDescriptorPath: /scripts/variantstore/wdl/test/GvsBenchmarkExtractTask.wdl
      filters:
          branches:
              - master
@@ -200,7 +200,7 @@ workflows:
              - /.*/
    - name: GvsCreateVATfromVDS
      subclass: WDL
-     primaryDescriptorPath: /scripts/variantstore/wdl/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
@@ -285,7 +285,7 @@ workflows:
              - /.*/
    - name: GvsQuickstartVcfIntegration
      subclass: WDL
-     primaryDescriptorPath: /scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl
+     primaryDescriptorPath: /scripts/variantstore/wdl/test/GvsQuickstartVcfIntegration.wdl
      filters:
          branches:
              - master
@@ -294,7 +294,7 @@ workflows:
              - /.*/
    - name: GvsQuickstartHailIntegration
      subclass: WDL
-     primaryDescriptorPath: /scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
+     primaryDescriptorPath: /scripts/variantstore/wdl/test/GvsQuickstartHailIntegration.wdl
      filters:
          branches:
              - master
@@ -303,7 +303,7 @@ workflows:
              - /.*/
    - name: GvsQuickstartIntegration
      subclass: WDL
-     primaryDescriptorPath: /scripts/variantstore/wdl/GvsQuickstartIntegration.wdl
+     primaryDescriptorPath: /scripts/variantstore/wdl/test/GvsQuickstartIntegration.wdl
      filters:
          branches:
              - master
@@ -313,7 +313,7 @@ workflows:
              - /.*/
    - name: GvsIngestTieout
      subclass: WDL
-     primaryDescriptorPath: /scripts/variantstore/wdl/GvsIngestTieout.wdl
+     primaryDescriptorPath: /scripts/variantstore/wdl/test/GvsIngestTieout.wdl
      filters:
          branches:
              - master
@@ -358,21 +358,13 @@ workflows:
              - /.*/
    - name: GvsTieoutVcfMaxAltAlleles
      subclass: WDL
-     primaryDescriptorPath: /scripts/variantstore/wdl/GvsTieoutVcfMaxAltAlleles.wdl
+     primaryDescriptorPath: /scripts/variantstore/wdl/test/GvsTieoutVcfMaxAltAlleles.wdl
      filters:
        branches:
          - ah_var_store
          - master
        tags:
          - /.*/
-   - name: HailFromWdl
-     subclass: WDL
-     primaryDescriptorPath: /scripts/variantstore/wdl/HailFromWdl.wdl
-     filters:
-         branches:
-             - master
-         tags:
-             - /.*/
    - name: MitochondriaPipeline
      subclass: WDL
      primaryDescriptorPath: /scripts/mitochondria_m2_wdl/MitochondriaPipeline.wdl
@@ -448,7 +440,7 @@ workflows:
          - EchoCallset
    - name: GvsTieoutPgenToVcf
      subclass: WDL
-     primaryDescriptorPath: /scripts/variantstore/wdl/GvsTieoutPgenToVcf.wdl
+     primaryDescriptorPath: /scripts/variantstore/wdl/test/GvsTieoutPgenToVcf.wdl
      filters:
        branches:
          - ah_var_store

diff --git a/scripts/variantstore/docs/aou/AOU_DELIVERABLES.md b/scripts/variantstore/docs/aou/AOU_DELIVERABLES.md
@@ -111,7 +111,7 @@ 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.
 
 Once the VAT table is created and a tsv is exported, the AoU research workbench team should be notified of its creation and permission should be granted so that several members of the team have view permission.

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/.../variantstore/wdl/GvsCreateVATfromVDS.wdl → ...annotations-table/GvsCreateVATfromVDS.wdl b/.../variantstore/wdl/GvsCreateVATfromVDS.wdl → ...annotations-table/GvsCreateVATfromVDS.wdl
@@ -1,7 +1,7 @@
 version 1.0
 
-import "GvsUtils.wdl" as Utils
-import "../variant_annotations_table/GvsCreateVATFilesFromBigQuery.wdl" as GvsCreateVATFilesFromBigQuery
+import "../wdl/GvsUtils.wdl" as Utils
+import "GvsCreateVATFilesFromBigQuery.wdl" as GvsCreateVATFilesFromBigQuery
 
 workflow GvsCreateVATfromVDS {
     input {

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/wdl/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
diff --git a/scripts/variantstore/wdl/HailFromWdl.wdl b/scripts/variantstore/wdl/HailFromWdl.wdl
diff --git a/.../variantstore/wdl/ImportArrayManifest.wdl → ...iantstore/wdl/old/ImportArrayManifest.wdl b/.../variantstore/wdl/ImportArrayManifest.wdl → ...iantstore/wdl/old/ImportArrayManifest.wdl
@@ -1,6 +1,6 @@
 version 1.0
 
-import "GvsUtils.wdl" as Utils
+import "../GvsUtils.wdl" as Utils
 
 workflow ImportArrayManifest {