testing something, please ignore

.dockstore.yml

@@ -5,56 +5,291 @@ workflows:
      primaryDescriptorPath: /scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl
      testParameterFiles:
      -  /scripts/cnv_cromwell_tests/germline/cnv_germline_case_scattered_workflow.json
+     filters:
+       branches:
+        - master
    - name: cnv_germline_cohort_workflow
      subclass: WDL
      primaryDescriptorPath: /scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl
      testParameterFiles:
      -  /scripts/cnv_cromwell_tests/germline/cnv_germline_cohort_workflow.json
+     filters:
+       branches:
+         - master
    - name: cnv_somatic_pair_workflow
      subclass: WDL
      primaryDescriptorPath: /scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl
-     testParameterFiles: 
+     testParameterFiles:
      -  /scripts/cnv_cromwell_tests/somatic/cnv_somatic_pair_wes_do-gc_workflow.json
+     filters:
+       branches:
+         - master
    - name: cnv_somatic_panel_workflow
      subclass: WDL
      primaryDescriptorPath: /scripts/cnv_wdl/somatic/cnv_somatic_panel_workflow.wdl
      testParameterFiles:
      -  /scripts/cnv_cromwell_tests/somatic/cnv_somatic_panel_wes_do-gc_workflow.json
+     filters:
+       branches:
+         - master
    - name: cram2filtered
      subclass: WDL
      primaryDescriptorPath: /scripts/cnn_variant_wdl/cram2filtered.wdl
      testParameterFiles:
      - /scripts/cnn_variant_wdl/jsons/cram2filtered.json
+     filters:
+       branches:
+         - master
    - name: cram2model
      subclass: WDL
      primaryDescriptorPath: /scripts/cnn_variant_wdl/cram2model.wdl
      testParameterFiles:
      - /scripts/cnn_variant_wdl/jsons/cram2model.json
+     filters:
+       branches:
+         - master
    - name: funcotator
      subclass: WDL
      primaryDescriptorPath: /scripts/funcotator_wdl/funcotator.wdl
      testParameterFiles:
      - /scripts/funcotator_wdl/funcotator.json
+     filters:
+       branches:
+         - master
+   - name: GvsAssignIds
+     subclass: WDL
+     primaryDescriptorPath: /scripts/variantstore/wdl/GvsAssignIds.wdl
+     testParameterFiles:
+       - /scripts/variantstore/wdl/GvsAssignIds.example.inputs.json
+     filters:
+       branches:
+         - master
+         - ah_var_store
+   - name: GvsAoUReblockGvcf
+     subclass: WDL
+     primaryDescriptorPath: /scripts/variantstore/wdl/GvsAoUReblockGvcf.wdl
+     filters:
+       branches:
+         - master
+         - ah_var_store
+   - name: GvsBenchmarkExtractTask
+     subclass: WDL
+     primaryDescriptorPath: /scripts/variantstore/wdl/GvsBenchmarkExtractTask.wdl
+     filters:
+       branches:
+         - master
+         - ah_var_store
+   - name: GvsRescatterCallsetInterval
+     subclass: WDL
+     primaryDescriptorPath: /scripts/variantstore/wdl/GvsRescatterCallsetInterval.wdl
+     filters:
+       branches:
+         - master
+         - ah_var_store
+   - name: GvsCreateFilterSet
+     subclass: WDL
+     primaryDescriptorPath: /scripts/variantstore/wdl/GvsCreateFilterSet.wdl
+     testParameterFiles:
+       - /scripts/variantstore/wdl/GvsCreateFilterSet.example.inputs.json
+     filters:
+       branches:
+         - master
+         - ah_var_store
+         - gg_VS-695_RunPandSForVQSR_Lite
+   - name: GvsPopulateAltAllele
+     subclass: WDL
+     primaryDescriptorPath: /scripts/variantstore/wdl/GvsPopulateAltAllele.wdl
+     filters:
+       branches:
+         - master
+         - ah_var_store
+   - name: GvsCreateTables
+     subclass: WDL
+     primaryDescriptorPath: /scripts/variantstore/wdl/GvsCreateTables.wdl
+     testParameterFiles:
+       - /scripts/variantstore/wdl/GvsCreateTables.example.inputs.json
+     filters:
+       branches:
+         - master
+         - ah_var_store
+   - name: GvsExtractCallset
+     subclass: WDL
+     primaryDescriptorPath: /scripts/variantstore/wdl/GvsExtractCallset.wdl
+     filters:
+       branches:
+         - master
+         - ah_var_store
+         - gg_VS-695_RunPandSForVQSR_Lite
+   - name: GvsImportGenomes
+     subclass: WDL
+     primaryDescriptorPath: /scripts/variantstore/wdl/GvsImportGenomes.wdl
+     filters:
+       branches:
+         - master
+         - ah_var_store
+         - VS-816
+   - name: GvsPrepareRangesCallset
+     subclass: WDL
+     primaryDescriptorPath: /scripts/variantstore/wdl/GvsPrepareRangesCallset.wdl
+     testParameterFiles:
+       - /scripts/variantstore/wdl/GvsPrepareRangesCallset.example.inputs.json
+     filters:
+       branches:
+         - master
+         - ah_var_store
+   - name: GvsCreateVATfromVDS
+     subclass: WDL
+     primaryDescriptorPath: /scripts/variantstore/wdl/GvsCreateVATfromVDS.wdl
+     filters:
+       branches:
+         - master
+         - ah_var_store
+         - mc_nirvana_reference_disk
+   - name: GvsCreateVATFilesFromBigQuery
+     subclass: WDL
+     primaryDescriptorPath: /scripts/variantstore/variant_annotations_table/GvsCreateVATFilesFromBigQuery.wdl
+     filters:
+       branches:
+         - master
+         - ah_var_store
+   - name: GvsValidateVat
+     subclass: WDL
+     primaryDescriptorPath: /scripts/variantstore/variant_annotations_table/GvsValidateVAT.wdl
+     testParameterFiles:
+       - /scripts/variantstore/variant_annotations_table/GvsValidateVat.example.inputs.json
+     filters:
+       branches:
+         - master
+         - ah_var_store
+   - name: GvsExtractCohortFromSampleNames
+     subclass: WDL
+     primaryDescriptorPath: /scripts/variantstore/wdl/GvsExtractCohortFromSampleNames.wdl
+     filters:
+       branches:
+         - master
+         - ah_var_store
+   - name: GvsWithdrawSamples
+     subclass: WDL
+     primaryDescriptorPath: /scripts/variantstore/wdl/GvsWithdrawSamples.wdl
+     filters:
+       branches:
+         - master
+         - ah_var_store
+   - name: GvsUnified
+     subclass: WDL
+     primaryDescriptorPath: /scripts/variantstore/wdl/GvsUnified.wdl
+     filters:
+       branches:
+         - master
+         - ah_var_store
+   - name: GvsJointVariantCalling
+     subclass: WDL
+     primaryDescriptorPath: /scripts/variantstore/wdl/GvsJointVariantCalling.wdl
+     filters:
+       branches:
+         - master
+         - ah_var_store
+         - rsa_vs_831
+   - name: GvsJointVariantCallsetCost
+     subclass: WDL
+     primaryDescriptorPath: /scripts/variantstore/wdl/GvsJointVariantCallsetCost.wdl
+     filters:
+       branches:
+         - master
+         - ah_var_store
+   - name: GvsCalculatePrecisionAndSensitivity
+     subclass: WDL
+     primaryDescriptorPath: /scripts/variantstore/wdl/GvsCalculatePrecisionAndSensitivity.wdl
+     filters:
+       branches:
+         - master
+         - ah_var_store
+         - gg_VS-695_RunPandSForVQSR_Lite
+   - name: GvsQuickstartVcfIntegration
+     subclass: WDL
+     primaryDescriptorPath: /scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl
+     filters:
+       branches:
+         - master
+         - ah_var_store
+   - name: GvsQuickstartHailIntegration
+     subclass: WDL
+     primaryDescriptorPath: /scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
+     filters:
+       branches:
+         - master
+         - ah_var_store
+   - name: GvsQuickstartIntegration
+     subclass: WDL
+     primaryDescriptorPath: /scripts/variantstore/wdl/GvsQuickstartIntegration.wdl
+     filters:
+       branches:
+         - master
+         - ah_var_store
+         - vs_834_disentangle
+   - name: GvsIngestTieout
+     subclass: WDL
+     primaryDescriptorPath: /scripts/variantstore/wdl/GvsIngestTieout.wdl
+     filters:
+       branches:
+         - master
+         - ah_var_store
+   - name: GvsCallsetCost
+     subclass: WDL
+     primaryDescriptorPath: /scripts/variantstore/wdl/GvsCallsetCost.wdl
+     filters:
+       branches:
+         - master
+         - ah_var_store
+   - name: GvsExtractAvroFilesForHail
+     subclass: WDL
+     primaryDescriptorPath: /scripts/variantstore/wdl/GvsExtractAvroFilesForHail.wdl
+     filters:
+       branches:
+         - master
+         - ah_var_store
+   - name: GvsCallsetStatistics
+     subclass: WDL
+     primaryDescriptorPath: /scripts/variantstore/wdl/GvsCallsetStatistics.wdl
+     filters:
+       branches:
+         - master
+         - ah_var_store
    - name: MitochondriaPipeline
      subclass: WDL
      primaryDescriptorPath: /scripts/mitochondria_m2_wdl/MitochondriaPipeline.wdl
      testParameterFiles:
      -  /scripts/mitochondria_m2_wdl/test_mitochondria_m2_wdl.json
+     filters:
+       branches:
+         - master
    - name: mutect2
      subclass: WDL
      primaryDescriptorPath: /scripts/mutect2_wdl/mutect2.wdl
      testParameterFiles:
      - /scripts/m2_cromwell_tests/mutect2.inputs.json
+     filters:
+       branches:
+         - master
    - name: mutect2_pon
      subclass: WDL
      primaryDescriptorPath: /scripts/mutect2_wdl/mutect2_pon.wd
+     filters:
+       branches:
+         - master
    - name: run_happy
      subclass: WDL
      primaryDescriptorPath: /scripts/cnn_variant_wdl/run_happy.wdl
      testParameterFiles:
      - /scripts/cnn_variant_wdl/jsons/run_happy.json
+     filters:
+       branches:
+         - master
    - name: pathseq_pipeline
      subclass: WDL
      primaryDescriptorPath: /scripts/pathseq/wdl/pathseq_pipeline.wdl
      testParameterFiles:
      - /scripts/pathseq/wdl/pathseq_pipeline_template.json
+     filters:
+       branches:
+         - master

.gitattributes

@@ -5,8 +5,7 @@ src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg38
 src/test/resources/large/funcotator/funcotator_dataSources/familial/hg38 -filter=lfs -diff=lfs -merge=lfs -text
 src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg38 -filter=lfs -diff=lfs -merge=lfs -text
 src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg38 -filter=lfs -diff=lfs -merge=lfs -text
-
 #Otherwise, track everything in large
 src/test/resources/large/** filter=lfs diff=lfs merge=lfs -text
 src/main/resources/large/** filter=lfs diff=lfs merge=lfs -text
-
+*.psd filter=lfs diff=lfs merge=lfs -text

.github/actions/install-cromwell/action.yml

@@ -0,0 +1,19 @@
+name: 'install-cromwell'
+description: 'installs cromwell and womtool locally for jobs that require it (and sets their paths as environment variables)'
+inputs:
+  CROMWELL_VERSION:  # id of input
+    description: 'Cromwell Version to download'
+    required: true
+runs:
+  using: "composite"
+  steps:
+    - name: Set Cromwell env variables
+      run: |
+        echo "CROMWELL_JAR=${HOME}/cromwell-${{ inputs.CROMWELL_VERSION }}.jar" >> $GITHUB_ENV;
+        echo "WOMTOOL_JAR=${HOME}/womtool-${{ inputs.CROMWELL_VERSION }}.jar" >> $GITHUB_ENV;
+      shell: bash
+    - name: Download Cromwell and Womtools
+      run: |
+        wget -q -O $CROMWELL_JAR https://github.com/broadinstitute/cromwell/releases/download/${{ inputs.CROMWELL_VERSION }}/cromwell-${{ inputs.CROMWELL_VERSION }}.jar;
+        wget -q -O $WOMTOOL_JAR https://github.com/broadinstitute/cromwell/releases/download/${{ inputs.CROMWELL_VERSION }}/womtool-${{ inputs.CROMWELL_VERSION }}.jar;
+      shell: bash