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Convert to Nextflow strict syntax#5

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manuelesimi with Copilot wants to merge 2 commits into
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copilot/convert-script-to-strict-syntax
Draft

Convert to Nextflow strict syntax#5
manuelesimi with Copilot wants to merge 2 commits into
mainfrom
copilot/convert-script-to-strict-syntax

Convert to Nextflow strict syntax - add parentheses to method calls

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