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Nextflow: Grab workflow descriptions

See original GitHub issue

Feature Request

It would be great if Dockstore could auto-populate a few extra fields from Nextflow workflows which are sometimes available in the config metadata.

Desired behaviour

Description: manifest.description (example)

Author (in table view): manifest.author (example)

Note that Workflow Path: /nextflow.config is a little confusing, as the workflow is in the main.nf file (default filename - can be defined with workflow.mainScript), and it’s this that you execute, rather than the config file. I know I can change it manually, but if it’s pulled by default somewhere.

Apologies if these already happen, it could be that I’m simply being too impatient after clicking refresh on my GitHub repos 😀

Phil

┆Issue is synchronized with this Jira Bug ┆Issue Type: Bug ┆Fix Versions: Dockstore 1.6 ┆Sprint: Seabright Sprint 6 Ferry ┆Issue Number: DOCK-209

Issue Analytics

State:
Created 5 years ago
Comments:9 (4 by maintainers)

Top GitHub Comments

1reaction

denis-yuencommented, Feb 8, 2019

We ended up calling out to Nextflow separately too (it wasn’t clear due to our lack of groovy expertise how to separate just what we needed and we didn’t want to include all of Nextflow in our classpath) May need to optimize later, but this should get us compatibility with descriptions, etc. from nf-core

Limitation: We can’t use Nextflow to aid us in detecting what files are useful from a repo (i.e. in CWL, we start with the “entry”/primary descriptor and spider out to figure out what files in the repo are relevant)

1reaction

denis-yuencommented, Jan 8, 2019

Oh cool, that at least gives us a good starting point. Thanks for the tip!

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