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Separate long lines containing e.g. extensive maps and process calls with many inputs to increase code readability. Additionally, some minor formatting and harmonisation throughout.
Strict mode
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Collaborator
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I can investigate the OOM errors in the next days, but the merge conflicts are resolved now. So feel free to continue with the strict syntax implementation @fasterius |
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We have several strict syntax warnings for modules with templates, which is an issue with the syntax parser; see issue nextflow-io/nextflow#6777 and Slack discussion at https://nfcore.slack.com/archives/C04QR0T3G3H/p1769678574070939. Module binaries was proposed as a solution, but we should instead wait for a future version of the syntax parser. We should probably merge this PR as soon as everything but this problem is fixed, at which point the template issue should hopefully solve itself with a future parser version. |
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I think this PR is finished from the "strict syntax" point of view, @nictru, and we just need to solve the failing CI. |
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Agreed, we should ignore the unused variable warnings for now Regarding the OOM error in the CI, a long time ago, I deliberately reduced the memory limit of the I don't think it is worth digging into why this could be happening. I will just incrementally increase the test profile's memory limit until it works. I don't expect having to set it higher than 10GB. |
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One question, @fasterius: How can we ensure we continue to follow the strict syntax in future changes? Are you aware of any plans to include this in the CI as part of the template? |
Contributor
Yes, they will start linting for the strict syntax (and other upcoming changes); read more at https://nf-co.re/blog/2025/nextflow_syntax_nf-core_roadmap. |
Member
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.5.1. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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This continues #242