nf-core modules install support non nf-core structured pipelines
Nobody has claimed this yet.
- 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
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 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