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Lk update buildindices pairedtag docs #1493

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Lk update buildindices pairedtag docs #1493

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ekiernan
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This PR updates our documentation to reflect recent changes to the BuildIndices and Single-cell gene expression pipelines.

Specifically, it captures:
Updates to BuildIndices v4.0.0
Updates to Optimus to incude CellBender
Updates to PairedTag to change default multimapper to EM instead of Uniform

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Remember to squash merge!

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🔍Changelog Validation Results:

basename: missing operand
Try 'basename --help' for more information.
Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
All changelog files are valid for this release.

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🔍Version Validation Results:

basename: missing operand
Try 'basename --help' for more information.
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.

khajoue2
khajoue2 approved these changes Jan 31, 2025
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lgtm

nikellepetrillo
nikellepetrillo approved these changes Jan 31, 2025
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thank you liz!!

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@nikellepetrillo nikellepetrillo nikellepetrillo approved these changes

@khajoue2 khajoue2 khajoue2 approved these changes

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@ekiernan @khajoue2 @nikellepetrillo