Np update truth paths #1572

nikellepetrillo · 2025-04-15T23:34:07Z

Description

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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?

…nctionality

…pdate_truth_paths

github-actions · 2025-04-22T14:48:07Z

Remember to squash merge!

github-actions · 2025-04-22T14:48:19Z

🔍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 · 2025-04-22T14:48:20Z

🔍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 · 2025-04-22T14:48:41Z

Remember to squash merge!

github-actions · 2025-04-22T14:48:49Z

🔍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 · 2025-04-22T14:48:51Z

🔍Changelog Validation Results:

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

* PD-2945: Update slide-tags (#1567) * Np add tests peakcalling (#1578) * add peakcalling test * add peakcalling test * add peakcalling test * turn call caching off * turn call caching off * turn call caching off * turn call caching off * update input for peakcalling * add sci test for peakcalling (#1580) * add sci test for peakcalling * add sci test for peakcalling * add sci test for peakcalling * PD-2937: Update BestPractices.md (#1584) * PD-2950: Write up SlideTags documentation (#1581) * Rc 2880 warp and forking (#1586) * update WARP name * update WARP name * Document on Forking WARP and pushing to dockstore * Updated pipeline_versions.txt with all pipeline version information --------- Co-authored-by: Farzaneh Khajouei <[email protected]> Co-authored-by: GitHub Action <[email protected]> * update to new input paths * Updated pipeline_versions.txt with all pipeline version information * Updated pipeline_versions.txt with all pipeline version information * update to new input paths * temp copy sci inputs to plumbing for testing purposes only * PD-2939: Add philosophy section to the get-started page (#1587) * fix paths * fix paths * fix paths * fix paths * rearrange input json * update truth bucket interpretation logic * dont cancel runs for now * up memory in CollectAggregationMetrics * mor emem * mor emem * remove jsons * remove jsons --------- Co-authored-by: aawdeh <[email protected]> Co-authored-by: Robert Sidney Cox <[email protected]> Co-authored-by: Farzaneh Khajouei <[email protected]> Co-authored-by: GitHub Action <[email protected]>

github-actions · 2025-05-27T17:06:17Z

Remember to squash merge!

github-actions · 2025-05-27T17:06:27Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
IlluminaGenotypingArray.wdl has not been changed and needs updating
ExomeReprocessing.wdl has not been changed and needs updating
WholeGenomeReprocessing.wdl has not been changed and needs updating
ExomeGermlineSingleSample.wdl has not been changed and needs updating
WholeGenomeGermlineSingleSample.wdl has not been changed and needs updating
UltimaGenomicsWholeGenomeGermline.wdl has not been changed and needs updating
VariantCalling.wdl has not been changed and needs updating
ReblockGVCF.wdl has not been changed and needs updating
UltimaGenomicsWholeGenomeCramOnly.wdl has not been changed and needs updating
Some WDLs or changelog files need updating. See output for details.
validation_failed

github-actions · 2025-05-27T17:06:29Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
IlluminaGenotypingArray.changelog.md has not been changed and needs to be updated
ExomeReprocessing.changelog.md has not been changed and needs to be updated
WholeGenomeReprocessing.changelog.md has not been changed and needs to be updated
ExomeGermlineSingleSample.changelog.md has not been changed and needs to be updated
WholeGenomeGermlineSingleSample.changelog.md has not been changed and needs to be updated
UltimaGenomicsWholeGenomeGermline.changelog.md has not been changed and needs to be updated
VariantCalling.changelog.md has not been changed and needs to be updated
ReblockGVCF.changelog.md has not been changed and needs to be updated
UltimaGenomicsWholeGenomeCramOnly.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

.github/workflows/test_peakcalling.yml

* PD-2945: Update slide-tags (#1567) * Np add tests peakcalling (#1578) * add peakcalling test * add peakcalling test * add peakcalling test * turn call caching off * turn call caching off * turn call caching off * turn call caching off * update input for peakcalling * add sci test for peakcalling (#1580) * add sci test for peakcalling * add sci test for peakcalling * add sci test for peakcalling * PD-2937: Update BestPractices.md (#1584) * PD-2950: Write up SlideTags documentation (#1581) * Rc 2880 warp and forking (#1586) * update WARP name * update WARP name * Document on Forking WARP and pushing to dockstore * Updated pipeline_versions.txt with all pipeline version information --------- Co-authored-by: Farzaneh Khajouei <[email protected]> Co-authored-by: GitHub Action <[email protected]> * PD-2939: Add philosophy section to the get-started page (#1587) * updated run_ancestry population metadata tsv and filtering parameters (#1590) * RNA-seq alignment pipeline for All of Us * add macaque test input json (#1593) * add macaque test input json * Updated pipeline_versions.txt with all pipeline version information * add macaque test input json * gzip fastqs * increase ulimit * rerun * rerun * rerun * rerun * changelogs * Updated pipeline_versions.txt with all pipeline version information * changelogs --------- Co-authored-by: GitHub Action <[email protected]> * point to new exome inputs * move inputs for now * Updated pipeline_versions.txt with all pipeline version information * move inputs for now * Updated pipeline_versions.txt with all pipeline version information * Updated pipeline_versions.txt with all pipeline version information * move inputs for now * new inputs * new inputs * Updated pipeline_versions.txt with all pipeline version information * Jw ao u filterand qc variants (#1589) * Add filter and QC WDL and python script --------- Co-authored-by: GitHub Action <[email protected]> * dummy commit * PD-2997: Add tests for Slide-Tags pipeline (#1585) * test * test * Updated pipeline_versions.txt with all pipeline version information * test * test * test * test * test * test * test * fix * test * Updated pipeline_versions.txt with all pipeline version information * test * Updated pipeline_versions.txt with all pipeline version information * test * test * test * test * test * json * Updated pipeline_versions.txt with all pipeline version information * json * add inputs for call to the verifySlideTags wdl * remove id input to slidetags * point the inputs to the private bucket for now just so we have access to run tests * add new task to compare stuff in tarballs * change name of verifytask alias * compare csvs using threshold logic * compare csvs using threshold logic * indentation * indentation * indentation * indentation * new threshold * col specific thresholds * new csv2 task * calculate tsse metrics only if fragment data is available * verbose * verbose * no thresholds for csv * change threshold for eps * change threshold for eps * change threshold for eps * increare more thresholds * fix compareh5file task * fix compareh5file task * exclude some columns from tests. * exclude some columns from tests. * exclude some columns from tests. * exclude some columns from tests. * exclude some columns from tests. * rewrite without tolerances * rewrite without tolerances * move out of beta * Updated pipeline_versions.txt with all pipeline version information * move out of beta * fix * fix * fix imports * Updated pipeline_versions.txt with all pipeline version information * add slidetags changelog first release * Updated pipeline_versions.txt with all pipeline version information * add slidetags changelog first release --------- Co-authored-by: GitHub Action <[email protected]> Co-authored-by: npetrill <[email protected]> Co-authored-by: Nikelle Petrillo <[email protected]> * fix input * update inputs * fix inputs * delete --------- Co-authored-by: aawdeh <[email protected]> Co-authored-by: Robert Sidney Cox <[email protected]> Co-authored-by: Farzaneh Khajouei <[email protected]> Co-authored-by: GitHub Action <[email protected]> Co-authored-by: Elizabeth Kiernan <[email protected]> Co-authored-by: Jessica Way <[email protected]>

.github/workflows/test_slidetags.yml

jg np update input paths

…aths np update ug pipelines truth/inputs

Np jg input fix

* update input sources * remove pipefail * fix input

nikellepetrillo and others added 30 commits March 19, 2025 09:57

update dyanmic truth paths

c7701d4

update buckekt names

153c27f

update buckekt names

9913d47

update buckekt names

8d2b80c

update buckekt names

2d4021c

update buckekt names

ed60c07

add warp-pipeline-dev as billing project

316e448

try to fix results path

244fece

try to fix results path

aaec3d4

try to fix results path

1c801dd

fix truth path

2abe71f

fix truth path

c6d2b26

fix truth path

7a3de2d

fix truth path

10663a2

add --billing-project=warp-pipeline-dev

94647ad

--billing-project=terra-f8e3de20

e031748

cleaning up extra debugging code

daba981

cleaning up extra debugging code

92e3742

Merge branch 'develop' into np_update_truth_paths

b388e0e

Merge branch 'develop' into np_update_truth_paths

6707aee

update slideseq inputs to private bucket to test out dynamic truth fu…

7a4e1a0

…nctionality

Merge remote-tracking branch 'origin/np_update_truth_paths' into np_u…

100b0e4

…pdate_truth_paths

revert

2eef91b

update optimus sci inputs

755636f

update plumbing multi snss2

551e1e9

update slideseq sci and plumbing

8481de5

update snm3c

5346ce3

Merge branch 'develop' into np_snm3c_slideseq_ss2sn_update_inputs

e37e1fd

update snm3c

8c35fd0

updates

334dfba

Merge remote-tracking branch 'origin/np_update_truth_paths' into np_u…

7c41901

…pdate_truth_paths

nikellepetrillo closed this Apr 22, 2025

nikellepetrillo reopened this Apr 22, 2025

update imputation

24a1584

github-advanced-security bot found potential problems May 27, 2025

View reviewed changes

.github/workflows/test_peakcalling.yml Dismissed Show dismissed Hide dismissed

github-advanced-security bot found potential problems Jun 4, 2025

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.github/workflows/test_slidetags.yml Dismissed Show dismissed Hide dismissed

nikellepetrillo and others added 13 commits July 2, 2025 15:22

update sample name maps

ab5c90f

revert bge

5015700

revert gather_vcfs_high_memory.json

282e757

revert gather_vcfs_high_memory.json

7c57915

fix bge sci

6b1d0b3

update ug pipelines

490b171

Merge pull request #1627 from broadinstitute/np_jg_np_update_truth_paths

3fbb03b

jg np update input paths

add gs://gatk-best-practices to public bucket identifiers

39d262d

forgot some instances of broad-gotc

c8a89ef

fix VerifyNA12878.wdl

1066cdd

Merge pull request #1628 from broadinstitute/ultima_np_update_input_p…

4ceda45

…aths np update ug pipelines truth/inputs

Merge pull request #1631 from broadinstitute/np_jg_input_fix

8aa15f2

Np jg input fix

np update Reprocessing input paths (#1636)

4ac288d

* update input sources * remove pipefail * fix input

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nikellepetrillo commented Apr 15, 2025

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