add find/unpigz module

[BioWilko]

Add a module for decompressing a large number of gzipped files, theoretically without hitting the terminal argument limit

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[BioWilko]

Resubmitted due to making an embarrassing git mess on the previous PR (#7379), previous review by @jfy133 taken into account

[jfy133]

LGTM, would be good to get a second 👀 again, maybe from @maxulysse as he looked atthe other?

[mahesh-panchal]

We might be able to trim this. Let me have a think.

[mahesh-panchal]

I think this is over-complicating things a lot.

Can files be staged in a directory or is this breaking things?

See if this works for your use case:

process TASK {
    input:
    path files_in, stageAs: 'gzipped/*'

    script:
    prefix = task.ext.prefix?: 'meta'
    def args = task.ext.args ?: ''
    if( files_in.any{ file -> !file.name.endsWith('.gz') } ){
        error("All files provided to this module must be gzipped (and have the .gz extension).")
    }
    if( files_in.any{ file -> file.baseName.startsWith(prefix) } ) {
        error("No input files can start with the same name as the output prefix in the module FIND_UNPIGZ (currently '${prefix}'). Please choose a different one.")
    }
    """
    while IFS= read -r -d \$'\\0' file; do
        unpigz \\
            ${args} \\
            -cd \\
            --processes ${task.cpus} \\
            \$file \\
            > ${prefix}.\$( basename \$file .gz )
    done < <( find gzipped/ -name '*.gz' -print0 )
    """

    output:
    path "$prefix.*"
}

Edit, I just noticed there's a problem with file.name in this context. It's not stripping the directory name like it should to check the prefix. Use baseName instead.

[BioWilko]

Thanks for the suggestions @mahesh-panchal , that's far more elegant!