SLURM requeue test

main.nf

// Path to an input file, or a pattern for multiple inputs
// Note - $baseDir is the location of this workflow file main.nf
params.story = "$baseDir/../test_data/mobydick.txt"

stories = Channel.fromPath( params.story )

process uppercase {

    cpus 1

    input:
    file story from stories

    output:
    file "${story.name}.uppercase" into uppercased

    """
    cat "$story" | tr "[a-z]" "[A-Z]" > "${story.name}.uppercase"
    """

}

process tolines {

    cpus 1

    input:
    file uppercase from uppercased

    output:
    file "${uppercase.name}.tolines" into tolines

    """
    cat "$uppercase" | tr -cs "A-Z'" "\012"  > "${uppercase.name}.tolines"
    sleep 3600
    """

}

process wordcounts {

    // Publish the outputs we create here into the workflow output directory
    publishDir "$baseDir/output", mode: 'copy'

    input:
    file wordlines from tolines

    output:
    file "${wordlines.name}.wordcount"

    """
    cat "$wordlines" | sort | uniq -c | sort -n -r > "${wordlines.name}.wordcount"
    """
}