Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Updated wgs alignment qc to use version 4.2.4 (dev) #334

Merged
merged 3 commits into from
Sep 18, 2023
Merged

Updated wgs alignment qc to use version 4.2.4 (dev) #334

merged 3 commits into from
Sep 18, 2023

Conversation

alexiswl
Copy link
Member

@alexiswl alexiswl commented Aug 3, 2023

No description provided.

@alexiswl alexiswl requested a review from victorskl August 3, 2023 03:17
@alexiswl alexiswl self-assigned this Aug 3, 2023
@victorskl victorskl added the epic label Aug 3, 2023
@victorskl victorskl added this to the 2023.02 milestone Aug 3, 2023
victorskl
victorskl reviewed Aug 4, 2023
View reviewed changes
Copy link
Member

@victorskl victorskl left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

hey Alexis; reference tar accessible.

Looks like you haven't release new version yet that bears 4.2.4..?

ica workflows versions list wfl.ff6ca1789f4e4eb0982ea3e01407aca8
ID                                  	NAME 	LANGUAGE	STATUS	TIMECREATED
wfv.742991534f63401f9371fa15e5141168	3.9.3	CWL     	Draft 	2021-09-16 10:36:50.431 +1000 AEST
wfv.4b378a3d6460436380785ec7add25d1f	3.7.5	CWL     	Draft 	2021-06-22 10:54:20.58 +1000 AEST

Acknowledging that you will be

... retiring dragen-wgs-qc-pipeline

https://github.com/umccr/cwl-ica/blob/main/cwl-ica-catalogue.md#dragen-wgs-qc-pipeline

... replacing with dragen-alignment-pipeline

https://github.com/umccr/cwl-ica/blob/main/cwl-ica-catalogue.md#dragen-alignment-pipeline

Hence, expecting you will be rotating wfl ID there to harmonise/reflect changes better, Right..?

No pressure..! 😅

@victorskl victorskl mentioned this pull request Aug 7, 2023
Merged
1 task
@alexiswl
Updated workflow to dragen alignment pipeline
1956ec6 
* (over dragen wgs qc pipeline)

Since we are using this workflow for wgs and wts, wgs alignment qc was a misleading workflow.  There are no differences between the wgs qc workflow and the dragen alignment pipeline .
@victorskl
Copy link
Member

hey Alexis; just saying -- whenever you think ready, pls click "re-request review" .. then I will go through again.

@alexiswl
Copy link
Member Author

alexiswl commented Aug 9, 2023

Looks like you haven't release new version yet that bears 4.2.4..?

Sorry, updated workflow id in 1956ec6 to fix this.

$ ica workflows versions list "wfl.a3e19e590ed34a0fa0518718cb8a36cf"
ID                                      NAME    LANGUAGE        STATUS  TIMECREATED
wfv.8d4f7349a1c642febf1f75c8d7e1efa6    4.2.4   CWL             Draft   2023-08-03 12:01:22.186 +1000 AEST
wfv.3f2a250b212c4acc94a8f3ca61cf94bd    4.0.3   CWL             Draft   2022-10-04 16:26:32.762 +1100 AEDT
wfv.18857ca42ff347f9bb364a14796dd531    3.9.3   CWL             Draft   2021-09-16 10:34:57.832 +1000 AEST
wfv.f80bbd52779f414390701b1b7c069078    3.7.5   CWL             Draft   2021-06-17 22:04:42.754 +1000 AEST

@alexiswl alexiswl requested a review from victorskl August 9, 2023 05:12
@alexiswl
Copy link
Member Author

alexiswl commented Aug 9, 2023

Re-requested review

@alexiswl alexiswl changed the title Updated wgs alignment qc to use version 4.2.4 Updated wgs alignment qc to use version 4.2.4 (dev) Aug 9, 2023
@victorskl
Copy link
Member

Rope you in @reisingerf with latest trend, Flo.

Pls note we are retiring dragen-wgs-qc-pipeline and dragen-alignment-pipeline which now accept to handle both WGS & WTS alignment QC. Hence, higher abstract wgts_alignment_qc type is born...

victorskl
victorskl approved these changes Aug 9, 2023
View reviewed changes
Copy link
Member

@victorskl victorskl left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

LGTM!

@victorskl
Copy link
Member

Just asking (assuming) the workflow catalogue will be updated at some point up there in cwl-ica repo, right..?

@alexiswl
Copy link
Member Author

alexiswl commented Aug 9, 2023

Yep, catalog updates happen on PR approvals, but wgs alignment pipeline still in umccr/cwl-ica#383

@victorskl
Copy link
Member

Gotcha..!

@victorskl
Copy link
Member

Portal Release - Ocicat: Run WTS QC workflow through Portal before running Dragen WTS Tumor Only Workflow

This was referenced Aug 10, 2023
Merged
Merged
@victorskl
Copy link
Member

DRAGEN-4 upgrade is a go. Merging...

@victorskl victorskl merged commit b5a1eee into master Sep 18, 2023
1 check passed
@victorskl victorskl deleted the dev/dragen-alignment-qc branch September 18, 2023 02:26
victorskl added a commit that referenced this pull request Oct 16, 2023
@victorskl
Portal TF: Added wts_alignment_qc workflow type SSM parameter
9e903b2 
* This is mandatory for SecondaryAnalysisHelper construct. At the mo,
  both wgs_alignment_qc and wts_alignment_qc are pointing to the same
  DRAGEN workflow at ICA CWL.
* This fixes Ocicat e2e run issue at QC step in DEV.

Related
* #334
* umccr/data-portal-apis#611
@victorskl victorskl mentioned this pull request Oct 16, 2023
Merged
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@victorskl victorskl victorskl approved these changes

Assignees

@alexiswl alexiswl

Labels
epic
Projects
None yet
Milestone
2023.02
Development

Successfully merging this pull request may close these issues.
2 participants
@alexiswl @victorskl