Skip to content

Feature/use tmpdir gatk#73

Merged
ellendejong merged 10 commits intodevelopfrom
feature/use_tmpdir_gatk
Aug 1, 2023
Merged

Feature/use tmpdir gatk#73
ellendejong merged 10 commits intodevelopfrom
feature/use_tmpdir_gatk

Conversation

@ellendejong
Copy link
Contributor

@ellendejong ellendejong commented Jul 7, 2023 •
edited
Loading

  • Use --tmp-dir GATK4 tasks
  • Use --TMP_DIR GATK4 - Picard tasks.
  • Use java tmpdir (picard + gatk)

@ellendejong ellendejong requested a review from rernst July 19, 2023 07:26
@ellendejong ellendejong marked this pull request as ready for review July 19, 2023 07:26
@ellendejong ellendejong marked this pull request as draft July 20, 2023 06:38
rernst
rernst requested changes Jul 20, 2023
View reviewed changes
Copy link
Member

@rernst rernst left a comment

Choose a reason for hiding this comment

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

Some small inconsistencies. Did you check Picard behaviour? Since it is also developed by broad.

@ellendejong
Copy link
Contributor Author

ellendejong commented Jul 24, 2023

Some small inconsistencies. Did you check Picard behaviour? Since it is also developed by broad.

Added java tmpdir to PICARD.

@ellendejong ellendejong marked this pull request as ready for review July 24, 2023 08:57
@ellendejong ellendejong requested a review from rernst July 24, 2023 08:58
@ellendejong ellendejong merged commit 320a36e into develop Aug 1, 2023
@ellendejong ellendejong mentioned this pull request Aug 1, 2023
Merged
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@rernst rernst rernst approved these changes

Assignees

No one assigned

Labels

None yet

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

2 participants

@ellendejong @rernst