nf-core / nf-core/tools

nf-core modules install support non nf-core structured pipelines

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

Description

Description of feature

nf-core modules does not support importing from a modules repo or pipeline that does not conform to nf-core standards:

> nf-core modules --git-remote https://github.com/genepi/nf-gwas list remote

                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 2.9 - https://nf-co.re


CRITICAL 'org_path' key not present in .nf-core.yml 
> nf-core modules --git-remote https://github.com/epi2me-labs/wf-basecalling list remote

                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 2.9 - https://nf-co.re


CRITICAL 'org_path' key not present in .nf-core.yml     

We should support importing from other Nextflow pipelines that are hosted elsewhere.

There are lots of places that could go wrong. It sounds like a nightmare. See https://github.com/nextflow-io/nextflow/issues/4112 for a discussion about adding this to Nextflow.

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 command and reproduce the failures against genepi/nf-gwas and epi2me-labs/wf-basecalling. Read the linked Nextflow issue for the discussed constraints; done means non-nf-core hosted pipelines can be imported without the .nf-core.yml org_path error.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
bioinformatics, cli
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
25/100

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