Add automated tests for nf-core download
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 322
- Forks
- 255
- Avg merge
- 2d 3h
- Merged PRs (30d)
- 5
Description
Description of feature
As discussed on Slack, nf-core download started failing with the nf-core/rnaseq pipeline because the container definitions were non-standard and this broke the parsing code we have in tools here.
Firstly, we could add a --dry-run type option to the nf-core download command that just runs the function linked above and doesn't actually download anything. Secondly, we could add the nf-core download --dry-run <OTHER_OPTIONS> as a CI test to the pipeline template linting.yml file that checks that that the command works whenever the pipeline code is updated.
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 reading the parsing code in tools/download.py around the linked lines 466-485 and inspect the nf-core download command options. Then review the pipeline template's linting.yml file to understand how CI tests are added. Done means a dry-run option exercises parsing without downloading and a CI test verifies the command when pipeline code changes.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- ci-cd, cli, testing
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 42/100