PD-2863: Optimus with one Starsolo instance

[aawdeh]

Updated the code to eliminate sharding — now, only a single instance of alignment (Starsolo) is running. Removed tasks related to sharding and merging BAM files

• Removed boolean variable is_slidetags in Optimus and Slide-tags pipelines
• Removed tasks: FastqProcessing and MergeSortBamFiles
• Added parameters for STARsoloFastq task, including cpu_platform_star, mem_size_star, cpu_star, disk_star, limitBAMsortRAM_star, and outBAMsortingBinsN_star

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.

• Did you add inputs, outputs, or tasks to a workflow?
• Did you modify, delete or move: file paths, file names, input names, output names, or task names?
• If you made a changelog update, did you update the pipeline version number?

[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':
Multiome.wdl has not been changed and needs updating
SlideSeq.wdl has not been changed and needs updating
grep: /home/runner/work/warp/warp/pipelines/skylab/optimus/Optimus_One.changelog.md: No such file or directory
Optimus_One.wdl and Optimus_One.changelog.md do not have matching versions
Optimus.wdl has not been changed and needs updating
PairedTag.wdl has not been changed and needs updating
MultiSampleSmartSeq2SingleNucleus.wdl has not been changed and needs updating
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
SlideSeq.changelog.md has not been changed and needs to be updated
fatal: ambiguous argument '/home/runner/work/warp/warp/pipelines/skylab/optimus/Optimus_One.changelog.md': unknown revision or path not in the working tree.
Use '--' to separate paths from revisions, like this:
'git <command> [<revision>...] -- [<file>...]'
Optimus.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
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':
Multiome.wdl has not been changed and needs updating
SlideSeq.wdl has not been changed and needs updating
grep: /home/runner/work/warp/warp/pipelines/skylab/optimus/Optimus_One.changelog.md: No such file or directory
Optimus_One.wdl and Optimus_One.changelog.md do not have matching versions
Optimus.wdl has not been changed and needs updating
PairedTag.wdl has not been changed and needs updating
MultiSampleSmartSeq2SingleNucleus.wdl has not been changed and needs updating
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
SlideSeq.changelog.md has not been changed and needs to be updated
fatal: ambiguous argument '/home/runner/work/warp/warp/pipelines/skylab/optimus/Optimus_One.changelog.md': unknown revision or path not in the working tree.
Use '--' to separate paths from revisions, like this:
'git <command> [<revision>...] -- [<file>...]'
Optimus.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
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':
Multiome.wdl has not been changed and needs updating
SlideSeq.wdl has not been changed and needs updating
grep: /home/runner/work/warp/warp/pipelines/skylab/optimus/Optimus_One.changelog.md: No such file or directory
Optimus_One.wdl and Optimus_One.changelog.md do not have matching versions
Optimus.wdl has not been changed and needs updating
PairedTag.wdl has not been changed and needs updating
MultiSampleSmartSeq2SingleNucleus.wdl has not been changed and needs updating
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
SlideSeq.changelog.md has not been changed and needs to be updated
fatal: ambiguous argument '/home/runner/work/warp/warp/pipelines/skylab/optimus/Optimus_One.changelog.md': unknown revision or path not in the working tree.
Use '--' to separate paths from revisions, like this:
'git <command> [<revision>...] -- [<file>...]'
Optimus.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
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
SlideSeq.changelog.md has not been changed and needs to be updated
Optimus.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
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':
Multiome.wdl has not been changed and needs updating
SlideSeq.wdl has not been changed and needs updating
Optimus.wdl has not had its version updated
PairedTag.wdl has not been changed and needs updating
MultiSampleSmartSeq2SingleNucleus.wdl has not been changed and needs updating
Some WDLs or 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
SlideSeq.changelog.md has not been changed and needs to be updated
Optimus.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
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':
Multiome.wdl has not been changed and needs updating
SlideSeq.wdl has not been changed and needs updating
Optimus.wdl has not had its version updated
PairedTag.wdl has not been changed and needs updating
MultiSampleSmartSeq2SingleNucleus.wdl has not been changed and needs updating
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]

🔍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
Optimus.changelog.md has not been changed and needs to be updated
Multiome.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]

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.

[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.

[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]

🔍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.

[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.

[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]

🔍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.

[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.

[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.