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

Updating picard version in QC.wdl to avoid error with updated Platform Name (PL) in the SAM/BAM/CRAM file. #1257

Open
wants to merge 7 commits into
base: develop
Choose a base branch
from
Open

Updating picard version in QC.wdl to avoid error with updated Platform Name (PL) in the SAM/BAM/CRAM file. #1257

wants to merge 7 commits into from

Conversation

jiveshs98
Copy link

Description

Updating picard docker version in QC.wdl.

  • Changed the docker value from us.gcr.io/broad-gotc-prod/picard-cloud:2.26.10 to us.gcr.io/broad-gotc-prod/picard-cloud:3.1.1.
  • I noticed that the task ValidateSamFile failed for CRAMs that contained "ELEMENT" as PL value. However, this shouldn't be the case as "ELEMENT" was added as a recognized value in the SAM format specification in August 2022. (See Appendix B: SAM Version History at here .
  • So, proposing to update the docker version of picard cloud to 3.1.1 because it is the latest tag and was created after the aforementioned change to the SAM format specification. This would help to prevent unnecessary pipeline failures from QC.WDL.

@dsde-jenkins
Copy link
Collaborator

Can one of the admins verify this patch?

1 similar comment
@dsde-jenkins
Copy link
Collaborator

Can one of the admins verify this patch?

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@fleharty fleharty Awaiting requested review from fleharty

@gbggrant gbggrant Awaiting requested review from gbggrant

@kachulis kachulis Awaiting requested review from kachulis

@samuelklee samuelklee Awaiting requested review from samuelklee

At least 2 approving reviews are required to merge this pull request.

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
3 participants
@jiveshs98 @dsde-jenkins @nikellepetrillo