Close #6512

This PR fixes an apparent regression in 25.10. The following directives fail when they are specified with a closure that references a process input:

• accelerator
• arch
• publishDir

This has to do with how they are implemented in ProcessBuilder. Most directives aren't implemented explicitly, but these directives require explicit methods in order to handle named arguments.

I'm not sure why it works in 25.04 but not in 25.10, since the logic of these methods were not changed when they were moved to ProcessBuilder. I suspect it was being held together with some hidden Groovy magic 🤷

Test case derived from the issue:

params.analysis_output_dir = 'analysis_output_dir'
params.analysis_id = 'analysis_id'

workflow {
    TEST( tuple('individual_id', 'sample_id') )
}

process TEST {
    publishDir { dirProcessReads(individual_id, sample_id) }, mode: 'link'

    input:
    tuple val(individual_id), val(sample_id)

    script:
    """
    echo '${dirProcessReads(individual_id, sample_id)}'
    """
}

def dirProcessReads(individual_id, sample_id) { 
    return "${sampleBaseDir(individual_id, sample_id)}/processedReads"
}

def sampleBaseDir(individual_id, sample_id) {
    return "${params.analysis_output_dir}/${params.analysis_id}.${individual_id}.${sample_id}"
}

I added a simplified version of this to the e2e tests.