nf-core / nf-core/tools

modules test fails with custom repo unless extra parameters are added

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bug
Dominant language
Python
Stars
322
Forks
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Avg merge
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Merged PRs (30d)
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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

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. 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

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