auto-determine publish mode

[riederd]

nf-deseq2/nextflow.config

Line 10 in 19ccb77

publishDir = [path: 'results/dummy_check_input', mode: params.publish_dir_mode]

Here is an idea how we could auto determine the publish mode:

import java.nio.file.Files;

def get_publishMode(d) {

    def mode = "copy"

    file(d).mkdirs()

    testFile = file(workflow.workDir + "/.test")
    testFile.write("test")

    testLink = file(d + "/.test")

    try {
        Files.createLink(testLink, testFile);
        mode = "link"
    } catch (IOException e) {
       System.err.println("WARNING: using copy as publish mode, reason: " + e)
    }

    testLink.delete()
    testFile.delete()
    return mode
 }


process test {
       publishDir "/tmp/testDR",
           mode: get_publishMode("/tmp/testDR")

    output:
    file("test_out.txt")

    script:
    """
    echo "TEST" > test_out.txt
    """

}

[grst]

That's cool!

Two comments:

• we should test creating the link in the res_dir, as that might be on a different file system
• I think it would be best to set params.publish_dir_mode = "auto" per default and then use the function to figure out the mode. That would still allow to manually override it to something else if necessary.

[riederd]

• To your first point, this is done with that code. It tries to create a link from the workDir to the publishDir, which is what happens when nextflow publishes results. When workDir and publishDir are on different filesystems, then an error is thrown and copy is used to publish
• params.publish_dir_mode = "auto" is a nice idea