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Fix CLI param override in strict config parser#6377

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bentsherman merged 2 commits intomasterfrom
fix-config-v2-cli-params-override
Sep 3, 2025
Merged

Fix CLI param override in strict config parser#6377
bentsherman merged 2 commits intomasterfrom
fix-config-v2-cli-params-override

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Close #6363

This PR fixes a bug in the strict config parser, where CLI params were not overriding config defaults (e.g. --outdir and params.outdir).

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
@bentsherman bentsherman added this to the 25.10 milestone Sep 2, 2025
@bentsherman bentsherman requested a review from jorgee September 2, 2025 18:29
@bentsherman bentsherman requested a review from a team as a code owner September 2, 2025 18:29
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@bentsherman bentsherman merged commit e146b41 into master Sep 3, 2025
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@bentsherman bentsherman deleted the fix-config-v2-cli-params-override branch September 3, 2025 14:30
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with NXF_SYNTAX_PARSER=v2, outputDir value not parsed for reports

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