Caching not working for FRASER
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- Dominant language
- Nextflow
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Description
Description of the bug
Whilst debugging some issues with the final Multiqc process of the pipeline using the out-of-the-box test data, I came to notice that resuming 99% completed pipelines do not properly reuse cache for FRASER processes after FRASER_PSIVALUECALCULATION. Is this expected behavior?
See below an resumed run of a DROP pipeline that previously failed on the very last process:
Command used and terminal output
# With pre-existing cache that sucessfully ran the pipelien up until DROP:MULTIQC:
nextflow run main.nf -profile test,apptainer --outdir test/ -resume
Relevant files
No response
System Information
- OS: Rocky Linux 8.10 (Green Obsidian)
- Kernel: Linux 4.18.0-553.123.1.el8_10.x86_64
- Architecture: x86-64
- Scheduler: Slurm 22.05.3
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 reproducing the issue with nextflow run main.nf -profile test,apptainer --outdir test/ -resume using the out-of-the-box test data and pre-existing cache. Inspect the FRASER processes after FRASER_PSIVALUECALCULATION and the final DROP:MULTIQC step; done means a resumed run reuses the expected cache for those processes.
Written by the indexing model from the issue text.
Assessment
- Domain
- data-engineering
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 52/100