modules test fails with custom repo unless extra parameters are added
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- Dominant language
- Python
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Description
Description of the bug
I am working with a custom repo where the org_path is not nf-core. The command fails because to grab the org_path, it uses the default git-remote, which is git@github.com:nf-core/modules.git instead of my git-remote path. i can fix this by adding the --git-remote parameter, but i find this a bit cumbersome, especially since the org_path is already in a local file at the top level of my repo. i am not sure what use case would necessitate looking at the remote git rather than the local .nf-core.yml file -- can this behavior be changed for easier usage?
This issue is similar to #2426, which was resolved by using the local file, iirc
Command used and terminal output
$ nf-core modules test polysolver
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 2.12.dev0 - https://nf-co.re
CRITICAL Cannot find directory 'modules/nf-core/polysolver'. Should be TOOL/SUBTOOL or TOOL
System information
nextflow: 23.10.0
Hardware: HPC
Executor: local
OS: CentOS Linux
nf-core: 2.12.dev0
python: 3.10.8
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 at the entry point for nf-core modules test polysolver and inspect how it resolves org_path, comparing the local top-level .nf-core.yml with the default git remote. Reproduce the failure with a custom repository, then verify the command works without --git-remote while existing remote-based behavior remains intact.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- git, python
- Domain
- cli, tooling
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100