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Add ${params.XXX} and ${projectDir} interpolation when comparing schema and config default params values. - #4505
LouisLeNezet wants to merge 5 commits into
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${params.XXX} and ${projectDir} interpolation when comparing schema and config default params values.
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preparing a release atm and this feels like something I want to have tested a bit in the wild, so will have to wait for the next release |
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The regex is too constrained for my liking. I also think actual interpolation isn't yet supported in nf-schema.
| return value | ||
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| new_values = re.sub( | ||
| r"\$\{?params\.([A-Za-z0-9_]+)\}?", |
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This regex is pretty flaky in reality. AFAIK it's perfectly valid nextflow to have e.g.:
"${ params.myvalue}"
"${params.myvalue }"
"${ params.myvalue }"
All of which would fail this check. In general this sort of thing is why I dislike a lot of the manual handling of nextflow code we do in tools.
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I also think actual interpolation isn't yet supported in nf-schema.
This PR doesn't touch the assets schema, it's only for the pipeline nextflow config default parameters values.
This regex is pretty flaky in reality.
Indeed, I could relax the regex expression.
PR checklist
Closes #4504
CHANGELOG.mdis updateddocsis updated