outputDir can't be used as an implicit variable within a config

[SPPearce]

Bug report

outputDir can't be used as an implicit variable within a config.
This means it can't be used within report to set the location of the report dynamically.

Expected behavior and actual behavior

outputDir = "output_test"
report {
    enabled = true
    file    = "${outputDir}/pipeline_info/execution_report.html"
}

should put the report inside the outputDir, but instead gives

ERROR ~ Unknown config attribute `report.outputDir` 

Environment

• Nextflow version: 24.10.1

Additional context

Confirmed as an issue by @bentsherman :

I'm now seeing we forgot to add outputDir as an implicit variable in the config

[bentsherman]

Looks like this error only happens if outputDir isn't explicitly defined in the config. So the example you gave is actually the workaround until we get it fixed

[siddharthab]

I think even if we do declare a default value in the config, any interpolations within the config do not get the overridden value from the -output-dir CLI flag. So we will need more than f2e675d.

So something like the below will always write the report to a results directory regardless of the value of -output-dir.

report {
    enabled = true
    file    = "${outputDir}/pipeline_info/execution_report.html"
}

[bentsherman]

That's a good point. I believe the same issue exists with workDir, which can be set on the command line or in the config. The only difference is that you should never really need to reference the workDir in the config.

The broader issue IMO is that these report file paths are a rough edge. See for example #3626 and #5364 . I've long suspected that these report paths would be a lot easier to manage if they could be specified in the script somehow, maybe as part of the new workflow outputs. That way...

• you don't have to specify outputDir at all, just the relative path
• you can use runtime info like the run name, session id, etc in the report path

Need to think more on this problem.

[SPPearce]

I wanted to save the report file in two locations recently, but I wasn't able to do that with how it is currently specified.