-output-dir parameter is not recognized

[bounlu]

-output-dir is displayed in nextflow run -h menu but the actual pipeline is asking for -outdir.

$ nextflow run -h
Execute a pipeline project
Usage: run [options] Project name or repository url
  Options:
    -o, -output-dir
       Directory where workflow outputs are stored

nextflow run nf-core/rnaseq \
-revision dev \
-profile docker,test \
-output-dir './results/' \
-work-dir './work/'

ERROR ~ Validation of pipeline parameters failed!

 -- Check '.nextflow.log' file for details
The following invalid input values have been detected:

* Missing required parameter(s): outdir

$ nextflow info
  Version: 24.10.5 build 5935
  Created: 04-03-2025 17:55 UTC (05-03-2025 01:55 GMT+08:20)
  System: Mac OS X 15.3.1
  Runtime: Groovy 4.0.23 on OpenJDK 64-Bit Server VM 23.0.2+7
  Encoding: UTF-8 (UTF-8)

[luisas]

This is because you have to use --outdir parameter in the nf-core/rnaseq pipeline.

See https://github.com/nf-core/rnaseq/blob/b96a75361a4f1d49aa969a2b1c68e3e607de06e8/nextflow_schema.json#L13

[luisas]

So it is a requirement from the pipeline, and not an issue of nextflow :)

[bounlu]

Surely, my point is to suggest synchronisation between nf-core and nextflow for the parameters.

[bentsherman]

We do intend to unify them but it will take some time