nf-core / nf-core/tools

nf-core modules does not list modules in pipeline repo

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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

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

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 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

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