Ability to use 'name' attribute with path() output

[stevekm]

It would be nice if we could change the file output name in the output directive, the same way you can do with input, like this;

process FOO {
    tag "${id}"
    publishDir "${params.outdir}", mode: "copy"

    input:
    val(id)

    output:
    // THIS WORKS; path(".command.sh"), topic: commands
    // THIS does not work;
    tuple val(id), val(task.process), path(".command.sh", name: "${id}.${task.process}.txt"), topic: commands

    script:
    """
    """
}

Currently it seems you would have to do something like this;

publishDir "${params.outdir}", mode: "copy", overwrite: true, saveAs: { filename ->
            if (filename == ".command.sh"){
                return "${id}.${task.process}.command.txt"
            }
        return filename
    }

though that still does not actually propagate down through the output channel, so your downstream processes will be forced to do the renaming, or you would have to rename in a separate closure

(example method of renaming in a downstream method)

channel.topic("commands").collectFile(storeDir:"${params.collectDir}") { id, proc, cmdtxt ->
        return [ "${id}.${proc}.command.txt".replace(":", "_"), cmdtxt.text ]
    }

would be easier if it could be just embedded in the output directive

[bentsherman]

You could accomplish this in the script:

script:
"""
cp .command.sh ${id}.${task.process}.txt
"""

You shouldn't rename helper files because it can break the Nextflow runtime. Copying them is fine, but still a bit sketchy since these files are internal, they aren't like a public user-facing API

[stevekm]

my goal is to avoid doing it in the script section