TSPS-183 Beagle imputation hg38 wdl and associated support wdls #1333
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Can one of the admins verify this patch? |
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@mmorgantaylor is this still relevant? |
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@jessicaway yes this is our working branch for beagle imputation for the imputation service. cc @jsotobroad. Jess, would it be helpful for us to squash and rebase off of develop? |
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OK, no problem! Whatever works best is fine. We were just cleaning up PRs and thought we would check in. I don't think we have touched imputation much recently, so I don't anticipate any conflicts |
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🔍Changelog Validation Results: |
🔍Version Validation Results: |
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🔍Changelog Validation Results: |
🔍Version Validation Results: |
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🔍Version Validation Results: |
🔍Changelog Validation Results: |
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🔍Version Validation Results: |
🔍Changelog Validation Results: |
| # 1.0.0 | ||
| 2025-02-24 (Date of Last Commit) | ||
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| * * Initial public release of the ImputationBeagle pipeline. |
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| * * Initial public release of the ImputationBeagle pipeline. | |
| * Initial public release of the ImputationBeagle pipeline. |
| 2025-02-24 (Date of Last Commit) | ||
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| * * Initial public release of the ImputationBeagle pipeline. | ||
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| { | |||
| "ImputationBeagle.multi_sample_vcf": "gs://broad-gotc-test-storage/imputation_beagle/scientific/vcfs/NA12878_10_duplicate.merged.cleaned.vcf.gz", | |||
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i see that this path points to a vcf.gz in a scientific directory, is that expected?
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it is - the way the scientific test differs from plumbing is that scientific runs on all chromosomes, and plumbing only runs on on a couple smaller chromosomes. the input data files themselves are the same. is that acceptable? i think the plumbing runs in just over an hour.
| File ref_panel_bref3 | ||
| File genetic_map_file | ||
| String basename | ||
| String chrom # not needed if ref file has been chunked and you are using the entire chunk |
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if these are not needed, should they be optional inputs?
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ah these were comments from our collaborator when we were creating this WDL; they are indeed needed. I'll remove these comments since they're confusing.
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🔍Version Validation Results: |
🔍Changelog Validation Results: |
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Description
We are adding a new WDL, ImputationBeagle.wdl, that performs array imputation using the Beagle tool instead of minimac4, which is used by the existing Imputation.wdl.
Supporting PR in warp-tools for the Beagle docker: broadinstitute/warp-tools#114
Jira ticket: https://broadworkbench.atlassian.net/browse/TSPS-222
Checklist
If you can answer "yes" to the following items, please add a checkmark next to the appropriate checklist item(s) and notify our WARP documentation team by tagging either @ekiernan or @kayleemathews in a comment on this PR.