Picard modules fail when all memory used
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bug
- Dominant language
- Nextflow
- Stars
- 229
- Forks
- 141
- Avg merge
- 13h 41m
- Merged PRs (30d)
- 1
Description
Description of the bug
To prevent the error we need to allocate only a fraction of the available memory, see #272
Picard modules have been updated in the modules repository. Make sure they are updated also in the pipeline before next release.
Command used and terminal output
Relevant files
No response
System information
No response
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reading issue #272 and comparing the updated Picard modules in the modules repository with the versions used by the atacseq pipeline. Trace where Picard module resource settings are configured; done means the pipeline uses the updated modules and allocates only a fraction of available memory before the next release.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100