PD-2721: Add checks for empty cells #1353

aawdeh · 2024-08-06T20:13:15Z

Added input parameters min_threshold and max_threshold to Demultiplexing task to allow user to configure max and min threshold of cells to be removed.

Added error message to ensure that if all fastq files are removed to error out

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 documentation team by tagging either @ekiernan or @kayleemathews 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 · 2024-08-06T20:13:27Z

Remember to squash merge!

github-actions · 2024-08-06T20:13:36Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
snm3C.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

github-actions · 2024-08-06T20:13:36Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
snm3C.wdl has not had its version updated
Some WDLs or changelog files need updating. See output for details.
validation_failed

github-actions · 2024-08-06T20:29:47Z

Remember to squash merge!

github-actions · 2024-08-06T20:29:55Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
snm3C.wdl has not had its version updated
Some WDLs or changelog files need updating. See output for details.
validation_failed

github-actions · 2024-08-06T20:29:59Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
snm3C.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

…/warp into aa-emptyfilecheck

github-actions · 2024-08-06T20:31:13Z

Remember to squash merge!

github-actions · 2024-08-06T20:31:21Z

🔍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 · 2024-08-06T20:31:25Z

🔍Changelog Validation Results:

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

ekiernan

thank you!

github-actions · 2024-08-07T15:54:06Z

Remember to squash merge!

github-actions · 2024-08-07T15:54:20Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
snm3C.wdl has not had its version updated
Some WDLs or changelog files need updating. See output for details.
validation_failed

github-actions · 2024-08-07T15:54:20Z

🔍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 · 2024-08-07T15:56:36Z

Remember to squash merge!

github-actions · 2024-08-07T15:56:49Z

🔍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 · 2024-08-07T15:56:49Z

🔍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 · 2024-08-09T13:39:37Z

Remember to squash merge!

github-actions · 2024-08-13T21:38:33Z

Remember to squash merge!

github-actions · 2024-08-13T21:38:45Z

🔍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 · 2024-08-13T21:38:46Z

🔍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 · 2024-08-13T21:56:17Z

Remember to squash merge!

github-actions · 2024-08-13T21:56:26Z

🔍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 · 2024-08-13T21:56:27Z

🔍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 · 2024-08-13T22:04:20Z

Remember to squash merge!

github-actions · 2024-08-13T22:04:30Z

🔍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 · 2024-08-13T22:04:33Z

🔍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 · 2024-08-13T22:04:38Z

Remember to squash merge!

github-actions · 2024-08-13T22:04:50Z

🔍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 · 2024-08-13T22:04:51Z

🔍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 · 2024-08-13T22:09:34Z

Remember to squash merge!

github-actions · 2024-08-13T22:09:44Z

🔍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 · 2024-08-13T22:09:49Z

🔍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 · 2024-08-14T13:59:16Z

Remember to squash merge!

github-actions · 2024-08-14T13:59:27Z

🔍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 · 2024-08-14T13:59:28Z

🔍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 · 2024-08-14T15:28:30Z

Remember to squash merge!

github-actions · 2024-08-14T15:28:40Z

🔍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 · 2024-08-14T15:28:42Z

🔍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.

Add if statements to check if cells are empty

44151bb

Add fail fast as optional boolean

a031745

Updated pipeline_versions.txt with all pipeline version information

8ce963a

Updated changelog

6ac097d

aawdeh added 2 commits August 6, 2024 16:30

Updated version number

600cfc2

Merge branch 'aa-emptyfilecheck' of https://github.com/broadinstitute…

ba3c33a

…/warp into aa-emptyfilecheck

Updated pipeline_versions.txt with all pipeline version information

ea4ab73

khajoue2 approved these changes Aug 7, 2024

View reviewed changes

ekiernan approved these changes Aug 7, 2024

View reviewed changes

Merge branch 'develop' into aa-emptyfilecheck

cde99ca

Updated pipeline_versions.txt with all pipeline version information

cca2d09

Update changelog and version

f039dd6

Updated pipeline_versions.txt with all pipeline version information

5c83028

added min/max threshold to remove cell level fastqs

eff9660

remove print statements

187aeb9

Added error when there are no files

0776935

Added print statements again

1ece9d9

tesT

7f6899f

tesT

bc44896

tesT

7185a9c

remove test statements

d90ca35

aawdeh merged commit 27f0e83 into develop Aug 14, 2024
11 checks passed

aawdeh deleted the aa-emptyfilecheck branch August 14, 2024 18:47

PD-2721: Add checks for empty cells #1353

PD-2721: Add checks for empty cells #1353

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aawdeh commented Aug 6, 2024 • edited Loading

Checklist

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🔍Version Validation Results:

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🔍Changelog Validation Results:

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🔍Changelog Validation Results:

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🔍Version Validation Results:

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🔍Changelog Validation Results:

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aawdeh commented Aug 6, 2024 •

edited

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