From 519a5583207d3aec206bc391be3ed6994944148f Mon Sep 17 00:00:00 2001 From: VJalili Date: Wed, 4 Oct 2023 14:08:04 -0400 Subject: [PATCH 1/2] Add .dockstore.yml. --- .github/.dockstore.yml | 73 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 73 insertions(+) create mode 100644 .github/.dockstore.yml diff --git a/.github/.dockstore.yml b/.github/.dockstore.yml new file mode 100644 index 000000000..d936f3dc7 --- /dev/null +++ b/.github/.dockstore.yml @@ -0,0 +1,73 @@ +version: 1.2 +workflows: + - subclass: WDL + name: 01-GatherSampleEvidence + primaryDescriptorPath: /wdl/GatherSampleEvidence.wdl + + - subclass: WDL + name: 02-EvidenceQC + primaryDescriptorPath: /wdl/EvidenceQC.wdl + + - subclass: WDL + name: 03-TrainGCNV + primaryDescriptorPath: /wdl/TrainGCNV.wdl + + - subclass: WDL + name: 04-GatherBatchEvidence + primaryDescriptorPath: /wdl/GatherBatchEvidence.wdl + + - subclass: WDL + name: 05-ClusterBatch + primaryDescriptorPath: /wdl/ClusterBatch.wdl + + - subclass: WDL + name: 06-GenerateBatchMetrics + primaryDescriptorPath: /wdl/GenerateBatchMetrics.wdl + + - subclass: WDL + name: 07-FilterBatchSites + primaryDescriptorPath: /wdl/FilterBatchSites.wdl + + - subclass: WDL + name: 08-PlotSVCountsPerSample + primaryDescriptorPath: /wdl/PlotSVCountsPerSample.wdl + + - subclass: WDL + name: 09-FilterBatchSamples + primaryDescriptorPath: /wdl/FilterBatchSamples.wdl + + - subclass: WDL + name: 10-MergeBatchSites + primaryDescriptorPath: /wdl/MergeBatchSites.wdl + + - subclass: WDL + name: 11-GenotypeBatch + primaryDescriptorPath: /wdl/GenotypeBatch.wdl + + - subclass: WDL + name: 12-RegenotypeCNVs + primaryDescriptorPath: /wdl/RegenotypeCNVs.wdl + + - subclass: WDL + name: 13-CombineBatches + primaryDescriptorPath: /wdl/CombineBatches.wdl + + - subclass: WDL + name: 14-ResolveComplexVariants + primaryDescriptorPath: /wdl/ResolveComplexVariants.wdl + + - subclass: WDL + name: 15-GenotypeComplexVariants + primaryDescriptorPath: /wdl/GenotypeComplexVariants.wdl + + - subclass: WDL + name: 16-CleanVcf + primaryDescriptorPath: /wdl/CleanVcf.wdl + + - subclass: WDL + name: 17-MainVcfQc + primaryDescriptorPath: /wdl/MainVcfQc.wdl + + - subclass: WDL + name: 18-AnnotateVcf + primaryDescriptorPath: /wdl/AnnotateVcf.wdl From e14b2092febe98aac4a1537e065dd7d45875f080 Mon Sep 17 00:00:00 2001 From: Vahid Date: Fri, 13 Oct 2023 06:33:50 -0700 Subject: [PATCH 2/2] Update .dockstore.yml --- .github/.dockstore.yml | 126 +++++++++++++++++++++++++++++++++++------ 1 file changed, 108 insertions(+), 18 deletions(-) diff --git a/.github/.dockstore.yml b/.github/.dockstore.yml index d936f3dc7..a934e932b 100644 --- a/.github/.dockstore.yml +++ b/.github/.dockstore.yml @@ -1,73 +1,163 @@ version: 1.2 workflows: - subclass: WDL - name: 01-GatherSampleEvidence + name: GatherSampleEvidence primaryDescriptorPath: /wdl/GatherSampleEvidence.wdl + filters: + branches: + - main + tags: + - /.*/ - subclass: WDL - name: 02-EvidenceQC + name: EvidenceQC primaryDescriptorPath: /wdl/EvidenceQC.wdl + filters: + branches: + - main + tags: + - /.*/ - subclass: WDL - name: 03-TrainGCNV + name: TrainGCNV primaryDescriptorPath: /wdl/TrainGCNV.wdl + filters: + branches: + - main + tags: + - /.*/ - subclass: WDL - name: 04-GatherBatchEvidence + name: GatherBatchEvidence primaryDescriptorPath: /wdl/GatherBatchEvidence.wdl + filters: + branches: + - main + tags: + - /.*/ - subclass: WDL - name: 05-ClusterBatch + name: ClusterBatch primaryDescriptorPath: /wdl/ClusterBatch.wdl + filters: + branches: + - main + tags: + - /.*/ - subclass: WDL - name: 06-GenerateBatchMetrics + name: GenerateBatchMetrics primaryDescriptorPath: /wdl/GenerateBatchMetrics.wdl + filters: + branches: + - main + tags: + - /.*/ - subclass: WDL - name: 07-FilterBatchSites + name: FilterBatchSites primaryDescriptorPath: /wdl/FilterBatchSites.wdl + filters: + branches: + - main + tags: + - /.*/ - subclass: WDL - name: 08-PlotSVCountsPerSample + name: PlotSVCountsPerSample primaryDescriptorPath: /wdl/PlotSVCountsPerSample.wdl + filters: + branches: + - main + tags: + - /.*/ - subclass: WDL - name: 09-FilterBatchSamples + name: FilterBatchSamples primaryDescriptorPath: /wdl/FilterBatchSamples.wdl + filters: + branches: + - main + tags: + - /.*/ - subclass: WDL - name: 10-MergeBatchSites + name: MergeBatchSites primaryDescriptorPath: /wdl/MergeBatchSites.wdl + filters: + branches: + - main + tags: + - /.*/ - subclass: WDL - name: 11-GenotypeBatch + name: GenotypeBatch primaryDescriptorPath: /wdl/GenotypeBatch.wdl + filters: + branches: + - main + tags: + - /.*/ - subclass: WDL - name: 12-RegenotypeCNVs + name: RegenotypeCNVs primaryDescriptorPath: /wdl/RegenotypeCNVs.wdl + filters: + branches: + - main + tags: + - /.*/ - subclass: WDL - name: 13-CombineBatches + name: CombineBatches primaryDescriptorPath: /wdl/CombineBatches.wdl + filters: + branches: + - main + tags: + - /.*/ - subclass: WDL - name: 14-ResolveComplexVariants + name: ResolveComplexVariants primaryDescriptorPath: /wdl/ResolveComplexVariants.wdl + filters: + branches: + - main + tags: + - /.*/ - subclass: WDL - name: 15-GenotypeComplexVariants + name: GenotypeComplexVariants primaryDescriptorPath: /wdl/GenotypeComplexVariants.wdl + filters: + branches: + - main + tags: + - /.*/ - subclass: WDL - name: 16-CleanVcf + name: CleanVcf primaryDescriptorPath: /wdl/CleanVcf.wdl + filters: + branches: + - main + tags: + - /.*/ - subclass: WDL - name: 17-MainVcfQc + name: MainVcfQc primaryDescriptorPath: /wdl/MainVcfQc.wdl + filters: + branches: + - main + tags: + - /.*/ - subclass: WDL - name: 18-AnnotateVcf + name: AnnotateVcf primaryDescriptorPath: /wdl/AnnotateVcf.wdl + filters: + branches: + - main + tags: + - /.*/