Use outputDir in nf-core pipelines
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@edmundmiller is already working on this.
Since Aug 8, 2025.
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Description
https://www.nextflow.io/docs/latest/workflow.html#publishing-files
In preparation for a larger migration when the new output syntax is stabilized, we'll need to add
outputDir = params.outdir
This will set it by default in a backwards-compatible way so people can continue using --outdir instead of migrating to -output-dir.
Would it also be worth adding linting to warn/fail if anyone uses params.outdir anywhere in their publishDir logic?
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