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Update Nextflow pipeline for strict variable parsing in NF version 26 #8

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@santy-ttam

Currently, we are by-passing the strict variable parsing used in Nextflow 26 by using export NXF_SYNTAX_PARSER=v1. In the future, the legacy parser will be removed and the strict parser will become the only way to run Nextflow code. We have to prepare for the strict parser by rewriting unsupported code with supported patterns

See link https://docs.seqera.io/nextflow/strict-syntax

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