nextflow-io / nextflow-io/nextflow
option to save/restore relative file paths
- Dominant language
- Groovy
- Stars
- 3.5k
- Forks
- 811
- Avg merge
- 2d 11h
- Merged PRs (30d)
- 61
Description
Currently, when a 'path' output of process A (e.g. param1/param2/data.csv) is passed as a 'path' input to a downstream process 'B', only the basename of the file (data.csv) is preserved; the path relative to task execution directory (param1/param2) is lost. This causes headaches whenever we adapt for Nextflow existing scripts that use paths to represent metadata. I often end up adding boilerplate code to manually save the full paths, pass them along as extra outputs, and restore them in subsequent steps. It would help if Nextflow had an option to save/restore the full relative paths automatically.
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
Review issue #3631 and the linked pull request #6905 first, then locate Nextflow's handling of path outputs passed to downstream path inputs. Confirm the intended option semantics and test cases for preserving and restoring relative paths; done means the relative path such as param1/param2/data.csv survives across processes without boilerplate.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- groovy
- Domain
- tooling
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 25/100