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.dockstore.yml
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version: 1.2
workflows:
- name: cnv_germline_case_scattered_workflow
subclass: WDL
primaryDescriptorPath: /scripts/cnv_wdl/germline/cnv_germline_case_scattered_workflow.wdl
testParameterFiles:
- /scripts/cnv_cromwell_tests/germline/cnv_germline_case_scattered_workflow.json
filters:
branches:
- master
tags:
- /.*/
- name: cnv_germline_case_workflow
subclass: WDL
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
tags:
- /.*/
- 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
tags:
- /.*/
- name: cnv_somatic_pair_workflow
subclass: WDL
primaryDescriptorPath: /scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl
testParameterFiles:
- /scripts/cnv_cromwell_tests/somatic/cnv_somatic_pair_wes_do-gc_workflow.json
filters:
branches:
- master
tags:
- /.*/
- 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
tags:
- /.*/
- name: cnv_joint_call_exomes
subclass: WDL
primaryDescriptorPath: /scripts/cnv_wdl/germline/joint_call_exome_cnvs.wdl
filters:
branches:
- master
tags:
- /.*/
- name: cram2filtered
subclass: WDL
primaryDescriptorPath: /scripts/cnn_variant_wdl/cram2filtered.wdl
testParameterFiles:
- /scripts/cnn_variant_wdl/jsons/cram2filtered.json
filters:
branches:
- master
tags:
- /.*/
- name: cram2model
subclass: WDL
primaryDescriptorPath: /scripts/cnn_variant_wdl/cram2model.wdl
testParameterFiles:
- /scripts/cnn_variant_wdl/jsons/cram2model.json
filters:
branches:
- master
tags:
- /.*/
- name: Funcotator
subclass: WDL
primaryDescriptorPath: /scripts/funcotator_wdl/funcotator.wdl
testParameterFiles:
- /scripts/funcotator_wdl/funcotator.json
filters:
branches:
- master
tags:
- /.*/
- name: GvsAssignIds
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsAssignIds.wdl
testParameterFiles:
- /scripts/variantstore/wdl/GvsAssignIds.example.inputs.json
filters:
branches:
- master
- ah_var_store
tags:
- /.*/
- name: GvsBenchmarkExtractTask
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/test/GvsBenchmarkExtractTask.wdl
filters:
branches:
- master
- ah_var_store
tags:
- /.*/
- name: GvsRescatterCallsetInterval
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsRescatterCallsetInterval.wdl
filters:
branches:
- master
- ah_var_store
tags:
- /.*/
- name: GvsCreateFilterSet
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsCreateFilterSet.wdl
testParameterFiles:
- /scripts/variantstore/wdl/GvsCreateFilterSet.example.inputs.json
filters:
branches:
- master
- ah_var_store
tags:
- /.*/
- name: GvsPopulateAltAllele
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsPopulateAltAllele.wdl
filters:
branches:
- master
- ah_var_store
tags:
- /.*/
- name: GvsCreateTables
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsCreateTables.wdl
testParameterFiles:
- /scripts/variantstore/wdl/GvsCreateTables.example.inputs.json
filters:
branches:
- master
- ah_var_store
tags:
- /.*/
- name: GvsCreateVDS
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsCreateVDS.wdl
filters:
branches:
- master
- ah_var_store
- vs_1418_ploidy_for_foxtrot_vds
tags:
- /.*/
- name: GvsValidateVDS
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsValidateVDS.wdl
filters:
branches:
- master
- ah_var_store
tags:
- /.*/
- name: GvsExtractCallset
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsExtractCallset.wdl
filters:
branches:
- master
- ah_var_store
tags:
- /.*/
- name: GvsImportGenomes
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsImportGenomes.wdl
filters:
branches:
- master
- ah_var_store
tags:
- /.*/
- name: GvsBulkIngestGenomes
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsBulkIngestGenomes.wdl
filters:
branches:
- master
- ah_var_store
tags:
- /.*/
- name: GvsPrepareRangesCallset
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsPrepareRangesCallset.wdl
testParameterFiles:
- /scripts/variantstore/wdl/GvsPrepareRangesCallset.example.inputs.json
filters:
branches:
- master
- ah_var_store
tags:
- /.*/
- name: GvsCreateVATfromVDS
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/variant-annotations-table/GvsCreateVATfromVDS.wdl
filters:
branches:
- master
- ah_var_store
- rc-1528-n-rounds-update
tags:
- /.*/
- name: GvsCreateVATFilesFromBigQuery
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/variant-annotations-table/GvsCreateVATFilesFromBigQuery.wdl
filters:
branches:
- master
- ah_var_store
tags:
- /.*/
- 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
tags:
- /.*/
- name: GvsExtractCohortFromSampleNames
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsExtractCohortFromSampleNames.wdl
filters:
branches:
- master
- ah_var_store
tags:
- /.*/
- name: GvsWithdrawSamples
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsWithdrawSamples.wdl
filters:
branches:
- master
- ah_var_store
tags:
- /.*/
- name: GvsJointVariantCalling
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsJointVariantCalling.wdl
filters:
branches:
- master
- ah_var_store
tags:
- /.*/
- name: GvsBeta
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsJointVariantCalling.wdl
filters:
branches:
# `master` is here so there will be *something* under the branches filter, but GVS WDLs are not on `master`
# so this shouldn't show up in the list of available versions in Dockstore or Terra.
- master
tags:
- /.*/
- name: GvsJointVariantCallsetCost
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsJointVariantCallsetCost.wdl
filters:
branches:
- master
- ah_var_store
tags:
- /.*/
- name: GvsCalculatePrecisionAndSensitivity
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsCalculatePrecisionAndSensitivity.wdl
filters:
branches:
- master
- ah_var_store
tags:
- /.*/
- name: GvsQuickstartVcfIntegration
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/test/GvsQuickstartVcfIntegration.wdl
filters:
branches:
- master
- ah_var_store
tags:
- /.*/
- name: GvsQuickstartHailIntegration
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/test/GvsQuickstartHailIntegration.wdl
filters:
branches:
- master
- ah_var_store
tags:
- /.*/
- name: GvsQuickstartIntegration
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/test/GvsQuickstartIntegration.wdl
filters:
branches:
- master
- ah_var_store
- vs_1609_edge_case
tags:
- /.*/
- name: GvsIngestTieout
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/test/GvsIngestTieout.wdl
filters:
branches:
- master
- ah_var_store
tags:
- /.*/
- name: GvsCallsetCost
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsCallsetCost.wdl
filters:
branches:
- master
- ah_var_store
tags:
- /.*/
- name: GvsExtractAvroFilesForHail
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsExtractAvroFilesForHail.wdl
filters:
branches:
- master
- ah_var_store
- rc-vs-1576-avro-update
tags:
- /.*/
- name: GvsCallsetStatistics
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsCallsetStatistics.wdl
filters:
branches:
- master
- ah_var_store
tags:
- /.*/
- name: GvsFindHailCruft
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsFindHailCruft.wdl
filters:
branches:
- master
- ah_var_store
tags:
- /.*/
- name: GvsTieoutVcfMaxAltAlleles
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/test/GvsTieoutVcfMaxAltAlleles.wdl
filters:
branches:
- ah_var_store
- master
tags:
- /.*/
- name: MitochondriaPipeline
subclass: WDL
primaryDescriptorPath: /scripts/mitochondria_m2_wdl/MitochondriaPipeline.wdl
testParameterFiles:
- /scripts/mitochondria_m2_wdl/ExampleInputsMitochondriaPipeline.json
filters:
branches:
- master
tags:
- /.*/
- name: mutect2
subclass: WDL
primaryDescriptorPath: /scripts/mutect2_wdl/mutect2.wdl
testParameterFiles:
- /scripts/m2_cromwell_tests/mutect2.inputs.json
filters:
branches:
- master
tags:
- /.*/
- name: mutect2_pon
subclass: WDL
primaryDescriptorPath: /scripts/mutect2_wdl/mutect2_pon.wdl
filters:
branches:
- master
tags:
- /.*/
- 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
tags:
- /.*/
- name: pathseq_pipeline
subclass: WDL
primaryDescriptorPath: /scripts/pathseq/wdl/pathseq_pipeline.wdl
testParameterFiles:
- /scripts/pathseq/wdl/pathseq_pipeline_template.json
filters:
branches:
- master
tags:
- /.*/
- name: GvsExtractCallsetPgen
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsExtractCallsetPgen.wdl
filters:
branches:
- master
- ah_var_store
- name: GvsExtractCallsetPgenMerged
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsExtractCallsetPgenMerged.wdl
filters:
branches:
- master
- ah_var_store
- name: MergePgenHierarchicalWdl
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/MergePgenHierarchical.wdl
filters:
branches:
- master
- ah_var_store
- name: GvsTieoutPgenToVcf
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/test/GvsTieoutPgenToVcf.wdl
filters:
branches:
- ah_var_store