develop -> staging - #1963
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* update sv pipeline to be consistent between task variable variable names and task command required input/output --------- Co-authored-by: Jose Soto <jsoto@broadinstitute.org> Co-authored-by: GitHub Action <action@github.com>
* Expose BWA machine-sizing inputs at Multiome top level ATAC sizes GetNumSplits/BWAPairedEndAlignment from num_threads_bwa (128) / mem_size_bwa (512) / cpu_platform_bwa, but Multiome.wdl only ever forwarded vm_size to ATAC -- these three were never top-level Multiome inputs at any point in git history. The only override path was Cromwell's nested-input mechanism (Multiome.Atac.num_threads_bwa), which a Terra method config exposing only the documented top-level inputs has no way to reach -- silently requesting an oversized 128 vCPU/512 GiB VM for every sample regardless of scale. Mirror the existing vm_size passthrough: add the three inputs with defaults unchanged from ATAC's own (no behavior change for existing configs), forward them into the Atac call. Thread them through the test wrapper too: TestMultiome.wdl now declares and forwards the three inputs, and the Multiome test_inputs JSONs move from the triple-nested Multiome.Atac.* form to the top-level Multiome.* form. The framework's UpdateTestInputs.py rewrites a 3-part key Multiome.Atac.num_threads_bwa -> TestMultiome.Multiome.Atac.num_threads_bwa, which validation rejects as an extra input; the 2-part top-level key rewrites to TestMultiome.num_threads_bwa, matching the new wrapper input. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * AGENTS.md: adding a pipeline input also requires threading tests The stale-input guidance was phrased for rename/remove only, so *adding* a top-level input slipped through: it fails at CI input-binding time (Extra inputs: ...) rather than breaking silently, and requires declaring + forwarding it in the Test<Name>.wdl wrapper, not just auditing the JSONs. Also document the UpdateTestInputs.py key rewrite (>2-part keys become TestPipeline.Pipeline.Sub.input and are rejected) and the resulting preference for top-level inputs. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> * Revert top-level BWA-sizing inputs; document nested-input workaround instead Rolls back exposing num_threads_bwa/mem_size_bwa/cpu_platform_bwa as top-level Multiome inputs (WDL, TestMultiome wrapper, test JSONs, changelog, pipeline_version bump) -- per decision to keep these as ATAC-internal, reachable only via Cromwell/Terra's nested-input override (Multiome.Atac.num_threads_bwa etc.), rather than growing Multiome's own input surface. In place of the code change, document the workaround directly in the Multiome docs: a :::warning callout under Inputs explaining that a run failing immediately at Atac.GetNumSplits/BWAPairedEndAlignment with no execution logs likely means the default 128 vCPU/512 GiB machine isn't available, and giving the nested-input JSON snippet to right-size it. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* add warp/website documentation for GLIMPSE2 SV wdl * update output variable names to be plural --------- Co-authored-by: Jose Soto <jsoto@broadinstitute.org>
* add vcf 4.X version header check to sv inputQC wdl --------- Co-authored-by: Jose Soto <jsoto@broadinstitute.org> Co-authored-by: GitHub Action <action@github.com>
* create version 1.0.0 release for sv imputation --------- Co-authored-by: Jose Soto <jsoto@broadinstitute.org> Co-authored-by: GitHub Action <action@github.com>
* Add MMIDAS pipelines
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Description
We want to release the v1.0.0. sv imputation wdl. This is the PR to get the develop branch into staging to eventually get staging into prod to perform the release
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 team by tagging @broadinstitute/warp-admins in a comment on this PR.