Dynamically build methods description from ch_versions #510
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jemten
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| if (toolDetails == null) { | ||
| throw new IllegalStateException("Tool: '${tool}' not found in ${references_yaml}") | ||
| } |
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Is this to make sure that each tool we run has an entry in the software_reference.yml file, even if the values are empty? Should we add this to the contribution doc?
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This is both to make sure we have an entry, but also because toolDetails[description] below will error with a less informative "can't get null value" or similar..
Good idea, will add to contribution doc!
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This PR adds a
software_references.ymland uses that together with the tools reported inch_versionsto dynamically write the methods description tools and references, depending on how subworkflows are skipped and params set.This should make the method description easier to maintain when adding or moving around tools and subworkflows. An error will also be produced if a new tool is added without an entry in
software_references.yml.Closes #508.
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).