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Compilation error for directory output directive #1

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byoo opened this issue Nov 21, 2024 · 1 comment
Open

Compilation error for directory output directive #1

byoo opened this issue Nov 21, 2024 · 1 comment

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@byoo
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byoo commented Nov 21, 2024

Hello, I'd like to report that nextflow 24.10.1 couldn't compile the workflow. This looks to be caused by the change in nextflow 24.10

https://nextflow.io/docs/latest/workflow.html#migrating-from-first-preview

The directory output directive has been replaced with the outputDir config option and -output-dir command line option, which is results by default. The other directives such as mode have been replaced with config options under workflow.output.*.

$ /software/nextflow/current/nextflow tumorNormalONT.nf 

 N E X T F L O W   ~  version 24.10.1

Launching `tumorNormalONT.nf` [happy_bhaskara] DSL2 - revision: 09395b075e

ERROR ~ Script compilation error
- file : /home/byoo/src/longread_somatic_nf/tumorNormalONT.nf
- cause: Invalid publish target definition @ line 88, column 5.
       directory params.outdir
       ^

1 error
@mikolmogorov
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Thanks Byunggil! Just wanted to confirm that we received this. We are making a lot of revisions in the pipeline now, and will test the newer Nexflow version as well.

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