galaxyproject / galaxyproject/galaxy

Format 2 - Allow Reports as second document in YAML

Open
#8,535 1 comment 0 reactions 0 assignees View on GitHub
area/workflows kind/enhancement
Dominant language
Python
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Forks
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Avg merge
2d 16h
Merged PRs (30d)
169

Description

@jxtx really likes the idea of workflow definitions as the "front-matter" to workflow report templates:

An example is here:

https://gist.github.com/jxtx/0525f0a9e1c7f903c21b12f7e29c1b31

The advantages are that it looks a lot like other popular formats (Rmd and Jekyll) and that you aren't embedded Markdown in YAML - which has its problems. My push back would just that it is slightly harder to parse documents that aren't strictly YAML and this would represent a serious divergence from CWL - which we've been trying to converge our workflow format with.

I don't think this is at all incompatible with embedding the workflow invocation report within the YAML so I think we can proceed with merge #8511 without this in place at first. This could probably be implemented 100% in the gxformat2 library after the fact.

Contributor guide

Open the contributing guide

Research direction

Review the linked gist and the gxformat2 library, then compare the proposal with merge #8511. The work is done when the proposed workflow-definition and report-document format is supported without embedding Markdown in YAML, with the parsing behavior documented and verified.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
backend
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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