nextflow-io / nextflow-io/nextflow
Cleanup after failed step
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- Dominant language
- Groovy
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Description
We want to cleanup some files used in out pipeline, since these tend to get quite big we would like to this both after a successfull and an errored step.
We tried using "afterScript" for this but this only seems to be triggered if a step was completed without error.
Question 1: is this the correct behaviour of a afterScript method
Question 2: is there a solution to cleanup files after a failed step in Nextflow. (we'd like to keep the working directory to resume the job using the successfull steps)
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
The issue names no files, tests, or entry points. Start by reproducing the afterScript behavior for both successful and failed Nextflow steps, then trace how failed-step working directories are retained for resume. Done means cleanup can run after failure without removing the files needed to resume successful steps.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- groovy
- Domain
- devtools
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Active
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100