Add new command nf-core rocrate to create a Research Object (RO) crate for a pipeline
#2680
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# Conflicts: # nf_core/__main__.py
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@nf-core-bot changelog: Add new command nf-core rocrate to create a Research Object (RO) crate for a pipeline |
| self.add_main_authors(wf_file) | ||
| wf_file.append_to("programmingLanguage", {"@id": "#nextflow"}) | ||
| # get keywords from nf-core website | ||
| remote_workflows = requests.get("https://nf-co.re/pipelines.json").json()["remote_workflows"] |
nf_core/rocrate.py
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| def add_main_authors(self, wf_file): | ||
| """ | ||
| Add workflow authors to the crate | ||
| NB: We don't have much metadata here - scope to improve in the future |
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Had some discussion about revisiting the CITATIONS.cff file and other things. For example, in theory I think that we can even associate ORCiD identifiers here and all sorts?
It'd also be cool if we could scrape GitHub contributors or something 🤔
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Nooo way, you did ORCiD lookups?? haha, amazing 🙇🏻
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added now all contributors to "main.nf" according to git (if they have an "identifiable" name (i.e. a space in it): e8959ef
nf_core/rocrate.py
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| Args: | ||
| path (Path): Path to the pipeline directory |
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| Args: | |
| path (Path): Path to the pipeline directory |
| # Conform to RO-Crate 1.1 and workflowhub-ro-crate | ||
| self.crate.update_jsonld( | ||
| { | ||
| "@id": "ro-crate-metadata.json", |
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Ifmetadata_fn is None, would this be an error?
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I changed the behavior of this parameter now to only be the path, because ro-crate-metadata.jsonseems to be the standard name for it.
| if fn.endswith(".png"): | ||
| log.debug(f"Adding workflow image file: {fn}") | ||
| self.crate.add_jsonld({"@id": Path(fn).name, "@type": ["File", "ImageObject"]}) | ||
| if "metro_map" in fn: |
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I think not everyone calls it "metro_map", should we add a point to the docs to let people know that they can use this in the file name?
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yeah, didn't come up with another good filter for it, but good point about the docs.
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TODO:
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Throws an error if downloaded using
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"Data entities representing workflows (@type: ComputationalWorkflow) SHOULD comply with the Bioschemas ComputationalWorkflow profile, where possible." - https://www.researchobject.org/ro-crate/1.1/workflows.html#complying-with-bioschemas-computational-workflow-profile |
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We could include subworkflows / modules information to the RO-Crate to increase machine readability. An overhead is of course the metadata size. Unclear situation with versioning: how to identify RO-Crates of a same workflow but of different versions (esp. if the changes are not yet commited to git) |
Example crate from the rnaseq pipeline:
ro-crate-metadata.json