nf-core / nf-core/funcprofiler
Any opportunities to delete intermediate files?
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- Dominant language
- Nextflow
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- 3
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- 2d 23m
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Description
Description of feature
Hello,
I've run into a problem where intermediate files have completely filled up our HPC's scratch space while using funcprofiler. I'm wondering if there are any opportunities to delete large unneeded files at the end of process scripts?
I can batch samples for now, but would be nice not to have to!
Thank you very much for your work on this pipeline!
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 tracing the pipeline's process scripts and the intermediate files they create during sample processing. Identify which large files are no longer needed after each process completes, then verify that cleanup reduces scratch usage without removing files required by later steps or final outputs.
Written by the indexing model from the issue text.
Assessment
- Domain
- hpc
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 45/100