I may be missing something, but I can't set

outputDir

to

params.outdir

https://nextflow.io/docs/latest/tutorials/workflow-outputs.html this works (in that the workflow output writes to

results2

)

test.conf:

outputDir = "${projectDir}/results2"

params {
  outdir = "${projectDir}/results1"
}

but this does not (it does not write to

results1

, it writes to the default

results

)

test.conf:
params {
  outdir = "${projectDir}/results1"
}

<http://main.nf|main.nf>:
nextflow.preview.output = true

workflow {
  outputDir = params.outdir
}
output { ...

and this also does not

test.conf:
params {
  outdir = "${projectDir}/results1"
}

<http://main.nf|main.nf>:
nextflow.preview.output = true

outputDir = params.outdir

workflow { ...
}
output { ...

Have you tried putting the parameters (i.e. whatever you have in

params{}

) in a JSON or YAML file and passing that to

nextflow

via

-params-file test.json

?

outputDir

is a configuration option. Can you try placing it in the nextflow.config?

Same as the first option, I think?

nextflow.config:

profiles {
    test {
        includeConfig 'conf/test.config'
    }
}

I need to overwrite that value with

params.outdir

though, since that is what nf-core/tower/seqera platform uses

You can see an example in one of my pipelines here: https://github.com/nf-cmgg/smallvariants/blob/7c074c45da18481e1ec54400f7d1d5267d67cb28/nextflow.config#L338

Hmm, thanks! Will give that a try. I am worried about order-of-declaration though, is params fully resolved at that point? Meanwhile, created an issue https://github.com/nextflow-io/nextflow/issues/6472 and found a possible workaround

nextflow.config:

// do not specify this!
outputDir = ""

test.config:

params {
  outdir = ${projectDir}/test-results
}

<http://main.nf|main.nf>:

workflow {
  ...
}
output {
  vcf {
    path {
      meta -> "${params.outdir}/vcf/${meta[0].id}"
    }
  }
}

I have had no issues with my pipelines. Interesting problem though!

that's a fun one

In the end, I could not get it to work when run from Seqera Platform so I went back to

projectDir

twitching eye