A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

FYI, I had some extra Claude usage over the 4th, and had Fable until today, and tried to come up with a non-bioinformatics-related coding problem to let it churn on.

So <https://github.com/nextflow-io/tree-sitter-nextflow|tree-sitter-nextflow> now parses all of nf-core/modules successfully :tada:

But what this really means is we can use <https://ast-grep.github.io/|ast-grep> for nf-core tools linting:
<https://github.com/nf-core/tools/pull/4377|github.com/nf-core/tools/pull/4377>

Which lets us have this <https://github.com/nf-core/tools/pull/4379/changes#diff-99ace1001204956ddcfb502b8d8f7d518649979d066ce96e4b51467c35a21f16|simple yaml per rule> with the regex/syntax and write transformations etc.

Stack of PRs
```  └─ #4377 Add AST-grep lint foundations
      └─ #4381 Migrate pipeline lint rules to AST-grep
         └─ #4378 Bump tree-sitter-nextflow parser pin
            └─ #4379 Flag legacy versions.yml topic outputs
               └─ #4380 Flag legacy versions emits```

waiting for it to be merged at the tree-sitter-first