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PD-2800: Add filtered option as output to MergeStarOutput task #1437

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PD-2800: Add filtered option as output to MergeStarOutput task #1437

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aawdeh
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@aawdeh aawdeh commented Nov 26, 2024

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?

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Remember to squash merge!

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@github-actions GitHub Actions
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Remember to squash merge!

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🔍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 GitHub Actions
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🔍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
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 GitHub Actions
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🔍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 GitHub Actions
Copy link

🔍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
SlideSeq.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

nikellepetrillo
nikellepetrillo reviewed Nov 27, 2024
View reviewed changes
tasks/skylab/StarAlign.wdl
@@ -623,6 +627,7 @@ task MergeStarOutput {
File? cell_reads_out = "~{input_id}.star_metrics.tar"
File? library_metrics="~{input_id}_library_metrics.csv"
File? mtx_files ="~{input_id}.mtx_files.tar"
File? filtered_mtx_files = "~{input_id}_filtered_mtx_files.tar"
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will outputbarcodes.tsv always exist? If not, will this line fail?

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Yes, the outputbarcodes.tsv file will still exist

@github-actions GitHub Actions
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Remember to squash merge!

@github-actions GitHub Actions
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🔍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 GitHub Actions
Copy link

🔍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.

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@nikellepetrillo nikellepetrillo nikellepetrillo left review comments

@rsc3 rsc3 rsc3 approved these changes

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@aawdeh @rsc3 @nikellepetrillo @actions-user