Update Syntax for Compatibility with Nextflow 23.04.4 #131
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Update syntax compatible with nextflow v23.04.4 for illumina workflow
Update syntax compatible with nextflow version 23.04.4
…tion of pangolin and freyja outputs.
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Description:
This pull request addresses the need to update the pipeline's syntax to ensure compatibility with more recent versions of Nextflow (e.g., 23.04.4) and presumably future versions. While the previous syntax worked with previous versions of Nextflow, further introduction of DSL2 features and syntax requirements in newer releases necessitate some adjustments.
Changes Made:
In this pull request, the following changes have been made:
main.nf:
Changed the syntax for enabling DSL2 for the pipeline using:
nextflow.enable.dsl = 2
modules/illumina.nf, modules/qc.nf, modules/upload.nf:
In these modules, I replaced instances where we used sampleName with val(sampleName). This change is necessary to make our code compatible with Nextflow version 23.04.4, which requires this specific syntax adjustment, as "Unqualified input value declaration has been deprecated". Additionally, I added explicit parentheses '()' around tuple arguments for consistency in code style.
Testing:
I have tested the updated pipeline on my local data and it performed as expected.
Request for Review:
I kindly request that the maintainers review these changes or provide feedback. It's crucial to ensure that these updates align with the project's goals and standards.
Possible Additional Changes:
Similar changes may be needed for other .nf files. As I focused on the --illumina workflow, i did not alter any other .nf files relating to nanopore processing.
Additional Information:
If you have any questions or need further clarification on any aspect of these changes, please feel free to reach out. I am committed to addressing any concerns and collaborating to ensure the successful integration of these updates.
Thank you for considering this pull request. Conforming the ncov2019-artic-nf pipeline with updated Nextflow versions should benefit future users of the pipeline.