Remove hyphens from pipeline names in Nextflow workflows

[adamrtalbot]

Description of feature

There's a common convention outside of nf-core to call your pipeline nf-${thing}, but in doing this we add a hyphen which is an invalid Nextflow workflow name.

It's an easy fix shortly after creation to remove the hyphen, but we can replace all hyphens with strings while creating the subworkflow names.

[adamrtalbot]

We could also reduce the number of workflows so this only affects one workflow in total, but this is a bigger issue.

I.e. the hierarchy would be from:

1. anonymous workflow (main.nf)
2. NF_CORE_PIPELINE_NAME (main.nf)
3. PIPELINE_NAME (workflows/main.nf)

To:

1. anonymous workflow (main.nf)
2. PIPELINE_NAME (workflows/main.nf)

Cut out the middle man workflow.

[colinbrislawn]

I just ran into this when using nf-core pipelines create

(I'm not sure if this is the best place to open pipelines create issues, so feel free to move or x-link this post!)

User story:

I'll make a new pipeline and I'll call it ex-ample !

Then, the first time I run it:

ERROR ~ Script compilation error
- file : github/colinbrislawn/ex-ample/main.nf
- cause: Not a valid include module name @ line 16, column 1.
   include { EX-AMPLE  } from './workflows/ex-ample'
   ^

Script compilation error
- file : github/colinbrislawn/ex-ample/main.nf
- cause: Workflow definition syntax error -- A string identifier must be provided after the `workflow` keyword @ line 28, column 9.
   workflow COLINBRISLAWN_EX-AMPLE {

[adamrtalbot]

@colinbrislawn the easy workaround is to replace all EX-AMPLE with EX_AMPLE in every *.nf file, which will fix the issue but preserve all the ex-ample pipeline names in other files like schemas etc. Straightforward with vscode, you can use find and replace.

Do it as a separate commit and Git will sort out template merging in future.

This shouldn't be too hard a problem to solve but someone needs to find time to do it.

[colinbrislawn]

Understood!

I left a comment because nf-core pipelines create generated invalid code and this is the closest existing issue I could find.

If there is a better place to put this story please let me know!

[awgymer]

We issue a warning:

Your workflow name is not lowercase without punctuation. This may cause Nextflow errors.\nConsider changing the name to avoid special characters.

But:

• only gets issued when you've already gone through the whole TUI and created the pipeline
• we know which characters will break nextflow (anything not covered by Java Identifiers AFAICT)

I am against silently munging people's chosen pipeline name but I don't see why we should continue allowing people to choose names which violate the known allowed set.

I am not sure how possible it is to add validation on the TextInput for workflow name in the TUI but at the very least I think we could migrate the current warning for nf-core pipelines into the same hard error as we use for nf-core pipelines.

[colinbrislawn]

I don't see why we should continue allowing people to choose names which violate the known allowed set.

👍

[adamrtalbot]

Repo names often have to obey a "standard", dictated by outside groups. If you're other programming team insist on calling everything {lang}-{proj}-{purpose} you don't get much choice in what it's called.

It’s straightforward to update the workflow name to ensure it’s syntactically correct without impacting anything outside the repository. In fact, the pipeline name isn’t required within the repository itself at all. Personally, I would name the workflow in workflows/main.nf as PIPELINE_NAME, as that’s the only instance where the pipeline name is referenced within the repository code.

[awgymer]

The repo name is far less linked to the concept of the pipeline than the name and code (and probably shouldn't be managed by nf-core anyway).

Would be easier to just leave that up to the people who need a custom repo name (which isn't tied to the pipeline at all anyway) rather than randomly changing the users' supplied pipeline name and maintaining the code logic which goes along with that.

As a kebab-case fan for repo names that's what I have always done anyway 🤷🏼‍♂️

[adamrtalbot]

That's exactly what this ticket is for. The nf-core tooling bakes in the pipeline name in many places, often putting it in a URL (e.g. github.com/org/pipeline-name). In the current form, the easiest thing is to create a pipeline with an invalid name (e.g. kebab case) then use the first commit to fix the workflow name.

From a recent template I made the pipeline name is used in:

• .nf-core.yml
• CHANGELOG
• main.nf*
• nextflow_schema.json
• nextflow.config
• README.md
• CONTRIBUTING.md
• feature_request.yml
• multiqc_config.yml
• base.config
• test.config
• test_full.config
• usage.md
• subworkflows/local/utils_{pipelinename}_pipeline*

Only the ones marked with an asterisk can be different from the repo name. By happy coincidence, they are also the ones that can't have a hyphen. I'd also argue the last one can be named something much better.