nf-core / nf-core/tools

User-selected branch used for upstream repo when updating modules from a forked subworkflow remote

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bug
Dominant language
Python
Stars
322
Forks
255
Avg merge
2d 3h
Merged PRs (30d)
5

Description

Description of the bug

Consider: a clean fork of nf-core/modules at https://github.com/organization/nf-core-modules.git, where the org is configured as my-organization. Feature branch feature/my-workflow provides the following:

  • subworkflow my-organization/my_subworkflow
    • component: module my-organization/mymodule/command1
    • component: module nf-core/fastqc

Running the command to update the subworkflow from this branch, and accepting the option to update all modules, causes a crash on updating fastqc. The root cause is that it tries to find branch feature/my-workflow on repo https://github.com/nf-core/modules.git, which does not exist.

Unable to provide actual terminal output due to my company's policy.

Command used and terminal output
$ nf-core subworkflows --git-remote https://github.com/organization/nf-core-modules.git --branch feature/my-workflow update my_subworkflow
System information

Python 3.12.8, Rocky Linux 9 on AWS, nf-core tools v4.0.2; nextflow version not applicable

Contributor guide

Open the contributing guide

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 with the nf-core subworkflows ... update my_subworkflow command and trace how --git-remote and --branch are applied while updating all modules. Reproduce the forked remote scenario with my-organization/mymodule and nf-core/fastqc; done means the selected branch is used for the forked repository without looking for that branch on the upstream nf-core/modules repository.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
cli
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Quiet
Clarity
Mostly clear
Newbie friendliness
65/100

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