publish two separate result directories from nextflow process

Question

I have a nextflow process that outputs a result folder and a log as below:

process test {
    label "x"

    input:
    path(somefile)

    output:
    path "test_results"
    path "test_log.log"
    path "something_for_next_process", emit: f

    shell:
    '''
    myshellcommand
    '''
}

And a config file to publish the results like below.

process
{
    withLabel : x
    {
        publishDir =
        [
            path: {"$params.outdir/"},
            pattern: "*_results",
            mode: 'copy',
            saveAs: {filename -> "${filename.split('_')[0]}/all_results/${filename.split("_")[1]}"}
        ]
    }
    withLabel : x
    {
        publishDir =
        [
            path: {"$params.outdir/"},
            pattern: "*.log",
            mode: 'copy',
            saveAs: {filename -> "${filename.split('_')[0]}/logs/${filename}"}
        ]
    }
}

I tried multiple combinations however, I can't get a label to publish its desired contents to two different folders. It always takes whichever is the last one in the publish config (in this case the logs). I know I can just put the publishdir options to the process in the workflow and that also works but I would like to do it through the config file. Is there a way I can get this to work?

Answer 1

You can specify the publishDir directive more than once in your nextflow.config by supplying a list of maps, for example:

process {

  withLabel: 'x' {

    publishDir = [
      [
        path: { "$params.outdir/" },
        pattern: "*_results",
        mode: 'copy',
        saveAs: { fn -> "${fn.split('_')[0]}/all_results/${fn.split("_")[1]}" }
      ],
      [
        path: { "$params.outdir/" },
        pattern: "*.log",
        mode: 'copy',
        saveAs: { fn -> "${fn.split('_')[0]}/logs/${fn}" }
      ]
    ]
  }
}

If you don't need the withName or withLabel process selectors, the publishDir directive can just be specified multiple times inside of your process definition, for example:

process test {

    publishDir(
        path: { "$params.outdir/" },
        pattern: "*_results",
        mode: 'copy',
        saveAs: { fn -> "${fn.split('_')[0]}/all_results/${fn.split("_")[1]}" }
    )
    publishDir(
        path: { "$params.outdir/" },
        pattern: "*.log",
        mode: 'copy',
        saveAs: { fn -> "${fn.split('_')[0]}/logs/${fn}" }
    )

    ...
}