ga4gh / ga4gh/cloud-interop-testing
Testbed targets
- Dominant language
- Python
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- Forks
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Description
Compiling a master list of workflows and environments for the Basel Testbed here. Once we get some of the basic information, we can add some more description/metadata.
### Workflows:
+ **TOPMed** (CWL, gs)
- [x] Registered in Dockstore? (version: [1.29.0](https://dockstore.org/workflows/github.com/DataBiosphere/topmed-workflows/TOPMed_alignment_pipeline_CWL:1.29.0?tab=info))
- [x] Checker workflow? (version: [1.29.0](https://dockstore.org/workflows/github.com/DataBiosphere/topmed-workflows/TOPMed_alignment_pipeline_CWL_cwl_checker:1.29.0?tab=info))
+ **TOPMed** (CWL, https)
- [x] Registered in Dockstore? (version: [1.31.0](https://dockstore.org/workflows/github.com/DataBiosphere/topmed-workflows/TOPMed_alignment_pipeline_CWL:1.31.0?tab=info))
- [x] Checker workflow? (version: [1.31.0](https://dockstore.org/workflows/github.com/DataBiosphere/topmed-workflows/TOPMed_alignment_pipeline_CWL_cwl_checker:1.31.0?tab=info))
+ **TOPMed** (WDL, gs)
- [x] Registered in Dockstore? (verison: [1.29.0](https://dockstore.org/workflows/github.com/DataBiosphere/topmed-workflows/u_of_Michigan_alignment_pipeline:1.29.0?tab=info))
- [x] Checker workflow? (version: [1.29.0](https://dockstore.org/workflows/github.com/DataBiosphere/topmed-workflows/u_of_Michigan_alignment_pipeline_wdl_checker:1.29.0?tab=info))
+ **TOPMed** (WDL, https)
- [x] Registered in Dockstore? (verison: [1.31.0](https://dockstore.org/workflows/github.com/DataBiosphere/topmed-workflows/u_of_Michigan_alignment_pipeline:1.31.0?tab=info))
- [x] Checker workflow? (version: [1.31.0](https://dockstore.org/workflows/github.com/DataBiosphere/topmed-workflows/u_of_Michigan_alignment_pipeline_wdl_checker:1.31.0?tab=info))
+ **HCA**
- [x] Registered in Dockstore? (version: [dockstore](https://dockstore.org/workflows/github.com/HumanCellAtlas/skylab/HCA_SmartSeq2:dockstore?tab=info))
- [x] Checker workflow? (version: [dockstore](https://dockstore.org/workflows/github.com/HumanCellAtlas/skylab/HCA_SmartSeq2_wdl_checker:dockstore?tab=info))
+ **AGHA** (CWL, gs) - *bcbio tumor/normal; SNPs indels and structural variants*
- [x] Registered in Dockstore? (version: [master](https://dockstore.org/workflows/github.com/bcbio/bcbio_validation_workflows/wes-agha-test-gcp:master?tab=info))
- [x] Checker workflow? (version: [master](https://dockstore.org/workflows/github.com/bcbio/bcbio_validation_workflows/wes-agha-test-gcp_cwl_checker:master?tab=info))
+ **AGHA** (CWL, keep) - *bcbio tumor/normal; SNPs indels and structural variants*
- [x] Registered in Dockstore? (version: [master](https://dockstore.org/workflows/github.com/bcbio/bcbio_validation_workflows/wes-agha-test-arvados:master?tab=info))
- [x] Checker workflow? (version: [master](https://dockstore.org/workflows/github.com/bcbio/bcbio_validation_workflows/wes-agha-test-arvados_cwl_checker:master?tab=info))
+ **ELIXIR**
- [ ] Registered in Dockstore? (version: )
- [ ] Checker workflow? (version: )
+ **Genomics England**
- [ ] Registered in Dockstore? (version: )
- [ ] Checker workflow? (version: )
### WES endpoints:
+ **TOPMed/HCA** via Broad (Cromwell)
- [x] Endpoint live? (url: http://35.226.102.121:9090)
- [x] Auth instructions documented/shared [with orchestrator]? (contact: @geoffjentry)
+ **HCA** via CZI (Cromwell)
- [x] Endpoint live? (url: https://tsilqioopd.execute-api.us-east-1.amazonaws.com/basel)
- [x] Auth instructions documented/shared [with orchestrator]? (contact: @mckinsel)
+ **AGHA** via Veritas (Arvados)
- [x] Endpoint live? (url: https://wes.qr1hi.arvadosapi.com)
- [x] Auth instructions documented/shared [with orchestrator]? (contact: @tetron)
+ **AGHA/GEL** via Illumina (Cromwell)
- [x] Endpoint live? (url: http://a102be3b8bc3b11e8b0d202055faded5-2029495258.us-west-2.elb.amazonaws.com)
- [x] Auth instructions documented/shared [with orchestrator]? (contact: @pr80ik)
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