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