Case Study
Working plan behind the manuscript’s Evidence section. The six requirements a worked case study must demonstrate are listed in the manuscript; this file tracks candidate fixtures and the open selection decisions.
Candidate fixtures
Pick one constrained conversion that yields the most checkable artifact (before GCC):
- A small nf-core pipeline or module path with representative channel semantics (exercises
summarize-nextflow→ Galaxy design Molds). - A CWL user-guide or bio-domain workflow summarized and translated into a Galaxy skeleton (exercises the CWL→Galaxy path; note current
summary-cwlnested-subworkflow gap when scoping). - A paper methods section with a narrow, well-known tool chain (exercises
summarize-paper→ Galaxy path).
Open decisions
- Which fixture, and how many. One is the floor; two distinct source axes (e.g. one Nextflow, one CWL) strengthens the breadth claim. Strongest case study is the one with the best artifact, not the most impressive biology.
- Emulation vs. automated run. A fully harness-automated run is the higher bar; an honestly-labelled agent-driven run may suffice for a first draft if the artifacts and validation are real. Decide framing before writing results.
- Biological weight. A recovered-signal or parameter-drift vignette is what a top venue (Genome Biology Software) wants; it is the PhD-contributor work flagged in the target ladder (
index.md).
What a result looks like
A results table (Molds exercised, validation outcome, any signal recovered/drift caught) plus the failure-comparison vignette. Artifacts (summary, briefs, gxformat2 draft, gxwf report) go to Supporting Information.