PD-2803: Fixing Optimus h5ad generation to handle gene_ids more flexibly

[ekiernan]

This PR updates the warp-tools docker for Optimus; this docker contains updated scripts for building the h5ad file. The script adds a more flexible search gene_name and gene_id to enable processing with refseq GTFs like those used for BICAN macaque and marmoset data processing. This should produce an h5ad file that has the appropriate gene_ids in the anndata.var.index.

[github-actions]

Remember to squash merge!

[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':
Multiome.changelog.md has not been changed and needs to be updated
PairedTag.changelog.md has not been changed and needs to be updated
Optimus.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.

[github-actions]

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
Multiome.changelog.md has not been changed and needs to be updated
PairedTag.changelog.md has not been changed and needs to be updated
Optimus.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':
atac.wdl has not had its version updated
Some WDLs or changelog files need updating. See output for details.
validation_failed

[github-actions]

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
Multiome.changelog.md has not been changed and needs to be updated
PairedTag.changelog.md has not been changed and needs to be updated
MultiSampleSmartSeq2SingleNucleus.changelog.md has not been changed and needs to be updated
Optimus.changelog.md has not been changed and needs to be updated
atac.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]

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
Multiome.changelog.md has not been changed and needs to be updated
PairedTag.changelog.md has not been changed and needs to be updated
Optimus.changelog.md has not been changed and needs to be updated
atac.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':
atac.wdl has not had its version updated
Some WDLs or changelog files need updating. See output for details.
validation_failed

[github-actions]

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
Multiome.changelog.md has not been changed and needs to be updated
PairedTag.changelog.md has not been changed and needs to be updated
Optimus.changelog.md has not been changed and needs to be updated
atac.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':
atac.wdl has not had its version updated
Some WDLs or 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]

Remember to squash merge!

[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.

[ekiernan]

retest this please