nf-core modules does not list modules in pipeline repo
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 322
- Forks
- 255
- Avg merge
- 2d 3h
- Merged PRs (30d)
- 5
Description
Description of the bug
I cannot use nf-core modules list on an nf-core pipeline repo.
See https://github.com/nextflow-io/nextflow/issues/4112 for a related discussion about importing modules from any pipeline and https://github.com/nf-core/tools/issues/2416 for a related improvement to tools.
Command used and terminal output
> nf-core modules --git-remote https://github.com/nf-core/rnaseq list remote
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 2.9 - https://nf-co.re
CRITICAL 'org_path' key not present in .nf-core.yml
Verbose:
nf-core --verbose modules --git-remote https://github.com/nf-core/rnaseq list remote
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 2.9 - https://nf-co.re
DEBUG Failed checking if running in CYGWIN due to: FileNotFoundError(2, 'No such file or directory') util.py:405
Pulling from 'nf-core/rnaseq' (https://github.com/nf-core/rnaseq) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Waiting for responseDEBUG Popen(['git', 'version'], cwd=/Users/adam.talbot/.config/nfcore/nf-core/rnaseq, universal_newlines=False, shell=None, istream=None) cmd.py:976
DEBUG Popen(['git', 'fetch', '-v', '--progress', '--', 'origin'], cwd=/Users/adam.talbot/.config/nfcore/nf-core/rnaseq, universal_newlines=True, shell=None, istream=None) cmd.py:976
DEBUG Popen(['git', 'checkout', 'master'], cwd=/Users/adam.talbot/.config/nfcore/nf-core/rnaseq, universal_newlines=False, shell=None, istream=None) cmd.py:976
DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/Users/adam.talbot/.config/nfcore/nf-core/rnaseq, universal_newlines=False, shell=None, istream=None) cmd.py:976
DEBUG Using config file: /Users/adam.talbot/.config/nfcore/nf-core/rnaseq/.nf-core.yml utils.py:1009
CRITICAL 'org_path' key not present in .nf-core.yml
System information
nf-core: 2.9
nextflow: 23.08.1-edge build 5874
python: 3.11.4
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 modules --git-remote ... list remote command path and the handling of .nf-core.yml, using the reproduced org_path error as the first failure to trace. Check the related Nextflow and nf-core/tools issues for expected behavior; done means listing modules from a pipeline repository without requiring an org_path key.
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
- 42/100