workflow is not defined in the config file

[zhilizheng]

Bug report

I tried to get the ${workflow.workDir} in the config file for trace path and name. Note the workDir and runName are specified by the nextflow run command line -w test -name test

trace{
    enabled = true
    file = "${workflow.workDir}/reports/${workflow.runName}.trace.txt"
}

Expected behavior and actual behavior

Expected: get the current work dir and runName specified by the command line
Actual: get an error:

ERROR ~ Unknown config attribute `workflow.workDir` -- check config file

Steps to reproduce the problem

Any job with the trace in config file, and specify the workDir and name by command line.

Program output

ERROR ~ Unknown config attribute `workflow.workDir` -- check config file:

Environment

• Nextflow version: [23.04.2]
• Java version: [17.0.8]
• Operating system: [Debian12]
• Bash version: (5.2.15)

[mribeirodantas]

One way to achieve such a thing in config files is through closures. You can get workflow.runName within a closure for publishDir.path. For example, check here. Unfortunately, trace.file doesn't evaluate closures 😢

@bentsherman

[pditommaso]

You can use a parameter to specify the work dir and reference in other settings

params.workDir = '/some/path'

workDir = params.workDir

trace{
    enabled = true
    file = "${params.workDir}/reports/etc.trace.txt"
}

[mateuszpawlik]

And what if I'd like to overwrite it from the command line? I'm trying but I can't make it work.

[stevekm]

hey just wanted to mention, I had similar issues as well recently, I threw together this little demo that shows different ways to dig out Nextflow implicit variables in a few different contexts, including within the nextflow.config, might be helpful for this discussion https://github.com/stevekm/nextflow-demos/tree/master/workflow-introspection