nf-core / nf-core/tools

Bioschemas Workflow Profile

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schema
Dominant language
Python
Stars
322
Forks
255
Avg merge
2d 3h
Merged PRs (30d)
5

Description

We are close to releasing our new pipeline schema which describe input parameters. Through chatting to people at BOSC 🍐 I've become aware of a project called Bioschemas which works with schema.org to publish official standardised ways to describe things.

They are currently developing a new schema standard which is specifically for computational workflows: https://bioschemas.org/profiles/Workflow/

Aspects of this schema seem to share a lot of overlap with the schema structure that we're working with already. It could be interesting to see if we can migrate our schema structure to the Bioschemas structure to adhere to this new community standard. This would help the visibility of the nf-core pipelines across the web and in other projects (eg. WorkflowHub).

This will be conditional on it being relatively fast and painless to implement and it still providing all of the functionality that we need (eg. custom fields, grouping of input parameters and so on).

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the Bioschemas Workflow profile and the existing pipeline schema referenced in the issue. Compare whether custom fields and grouped input parameters are supported, then establish a concrete migration scope and acceptance criteria. Done means the feasibility and required changes are agreed.

Written by the indexing model from the issue text.

Assessment

Domain
backend-api-design
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
22/100

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