Jw allen metadata changes

[jessicaway]

Description

This PR adds an optional input parameter that allows customization of the metadata field name used for the sample identifier stored in the H5AD outputs.

The Allen Institute requested that the identifier currently used in the H5AD output filenames (i.e. input_id) also be represented within the H5AD metadata itself. After review, we confirmed that this value is already included in the outputs under the "input_id" field.

This change makes the field name configurable so that workflows can label the value more appropriately (for example, as barcoded_cell_sample_local_name) when desired. By default, the field name remains input_id, which matches the current behavior and maintains backward compatibility.

---

The corresponding Warp-tools PR is here: broadinstitute/warp-tools#198

[github-actions]

Remember to squash merge!

[github-actions]

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
MultiSampleSmartSeq2SingleNucleus.changelog.md has not been changed and needs to be updated
SlideTags.changelog.md has not been changed and needs to be updated
PairedTag.changelog.md has not been changed and needs to be updated
SlideSeq.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

[github-actions]

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
All WDLs and changelog files appear to be valid for this release.

[Copilot]

Pull request overview

This PR introduces a new optional WDL input (input_id_name, default "input_id") to let callers customize the metadata key used to store the sample identifier in H5AD outputs, while preserving backward-compatible defaults. It threads that input through Optimus, Multiome, and ATAC H5AD-generation paths and updates associated pipeline versions/changelogs.

Changes:

• Added input_id_name inputs and passed them into H5AD creation steps (Optimus + ATAC; Multiome threads through to both).
• Bumped pipeline versions and updated pipeline_versions.txt for Optimus, Multiome, and ATAC; updated several warp-tools docker tags to 2.7.1.
• Minor repo hygiene/docs updates (AoU mitochondria changelog headings, .gitignore workspace entry).

Reviewed changes

Copilot reviewed 9 out of 10 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
tasks/wdl/H5adUtils.wdl	Adds input_id_name to Optimus-related H5AD tasks; updates default warp-tools docker tags for SmartSeq2 H5AD tasks.
pipelines/wdl/optimus/Optimus.wdl	Exposes input_id_name, threads it into OptimusH5adGeneration, bumps pipeline + warp-tools docker versions.
pipelines/wdl/optimus/Optimus.changelog.md	Adds 9.1.1 entry describing the new configurable H5AD metadata key.
pipelines/wdl/multiome/Multiome.wdl	Exposes input_id_name and threads it to both Optimus (GEX) and ATAC subworkflows; bumps pipeline version.
pipelines/wdl/multiome/Multiome.changelog.md	Adds 7.0.2 entry describing input_id_name passthrough.
pipelines/wdl/atac/atac.wdl	Exposes input_id_name, writes it into ATAC H5AD obs/uns, bumps pipeline + warp-tools docker versions.
pipelines/wdl/atac/atac.changelog.md	Adds 2.9.4 entry describing the new configurable H5AD metadata key.
pipeline_versions.txt	Updates recorded versions/dates for Optimus, Multiome, and atac.
all_of_us/mitochondria/merge/mitochondria_merge.changelog.md	Fixes missing Markdown headings for older AoU version entries.
.gitignore	Ignores warp.code-workspace.

[github-actions]

Remember to squash merge!

[github-actions]

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
All WDLs and changelog files appear to be valid for this release.

[github-actions]

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
SlideTags.changelog.md has not been changed and needs to be updated
PairedTag.changelog.md has not been changed and needs to be updated
SlideSeq.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

[github-actions]

Remember to squash merge!

[github-actions]

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
All WDLs and changelog files appear to be valid for this release.

[github-actions]

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
All changelog files are valid for this release.