fasterq-dump => disk: local-ssd
Nobody has claimed this yet.
- Dominant language
- Nextflow
- Stars
- 202
- Forks
- 93
- Avg merge
- 1d 18m
- Merged PRs (30d)
- 15
Description
Description of feature
As far as I can tell, the fasterqdump module does not set disk.
Setting the disk to local-ssd for use with google-batch could be quite helpful for speeding up the writing of temp files (docs).
More generally, if disk is not set (and dynamically expanded for large SRA files), what would prevent the job from running out of disk space -- at least for cloud jobs?
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 with modules/nf-core/sratools/fasterqdump/main.nf, then read the linked Nextflow disk reference and Google Cloud process documentation. Determine how the module should request local-ssd storage and whether disk needs dynamic sizing for large SRA files; the work is done when the cloud job has an adequate, documented disk configuration.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- google-cloud
- Domain
- cloud
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100