Subworkflow installation bug
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- Dominant language
- Python
- Stars
- 322
- Forks
- 255
- Avg merge
- 2d 3h
- Merged PRs (30d)
- 5
Description
Description of the bug
If you have paths as:
include { MY_SMALL_SUBWORKFLOW } from '../../../subworkflows/org/my_small_subworkflow/main.nf'
When you do nf-core module install of nf-core module update it looks for a module named modules/org/my/small/subworkflow, which does not exist, and therefore it errors out. What does exist is the subworkflow my_small_subworkflow.
To load a subworkflow inside a subworkflow during installation, the path must be:
include { MY_SMALL_SUBWORKFLOW } from '../my_small_subworkflow/main.nf'
I think both path strings should be allowed
Command used and terminal output
$nf-core subworkflows install my_big_subworkflow
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 2.13.1 - https://nf-co.re
INFO Reinstalling 'my_big_subworkflow'
ERROR Module 'my/small/subworkflow' not found in list of available modules.
System information
nf-core/tools version 2.13.1
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
Reproduce the problem with nf-core subworkflows install my_big_subworkflow using the two include paths shown in the issue, then trace the subworkflow installation entry point. Check that both path forms resolve to my_small_subworkflow rather than transforming the name into my/small/subworkflow; done means installation succeeds for both forms.
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
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100