More linter adventures

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1

In a previously fine nextflow.config file, a set of linting issues suddenly appeared.
In

params {
    // Timestamps config
    raw_timestamp = java.time.LocalDateTime.now()
    timestamp     = String.format('%tFT%<tH:%<tM', raw_timestamp)
    month_folder  = String.format('/%tY/%<tm', raw_timestamp)
}

the linter complains about raw_timestamp is not defined` in the two lines where it is used.

In

profiles {
    standard {
        process {
            executor = 'local'
            resourceLimits = [ cpus: params.max_cpus, memory: params.max_memory, time: params.max_time ]
        }
    }

    cluster {
        process {
            executor = 'slurm'
            resourceLimits = [ cpus: params.max_cpus, memory: params.max_memory, time: params.max_time ]
        }
        executor {
            jobName = { "PipelineName-${task.name.replaceAll(" ", "_")}" }
            queueSize = 20000
        }
    }
}

the definition of jobName in profiles.cluster.executor complains about Dynamic config options are only allowed in the 'process' scope. It also tells me that 'task' is not defined. Should I move that definition to the process scope above?

Finally, in

process {
    ...
    withName: 'PROCESS_NAME' {
        publishDir = [
            path: {
                meta.Name ?
                    "$params.outdir/$meta.Name"
                    : "$params.outdir/$meta.OtherName"
                },
            pattern: "*.report.json",
            mode: "link"
        ]
    }
    ...
}

it complains about 'meta' is not defined. How could I solve this?

All the definitions work flawlessly, so despite some things “not being defined”, the runtime finds it in place.