Add module PBMARKDUP

[sainsachiko]

Add pbmarkdup to identifies and marks duplicate reads in PacBio HiFi (CCS) data.
#9456
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[DLBPointon]

làm tốt lắm!

I just have a few comments to flesh it out more.

It'll mean adding another test, sorry. Feel free to get another opinion though.

[DLBPointon]

Change the bit about it being BAM output, as there are 3 formats it can output.

[DLBPointon]

I feel like the --dup-file dups.fasta flag needs better support, otherwise it won't get caught and output.

Perhaps an output channel, and something to capture the name the user will use in the config?

output:
tuple val(meta), path("${dup_file}"), optional: true, emit: duplicates

script:

// This little chunk would be soley to have a string to give to the output tuple
// not needed in the script as it exists in the args.
def matcher = (task.ext.args =~ /--dup-file\s+(\S+)/)
dup_file = matcher.find() ? matcher[0][1] : ""

"""
    pbmarkdup \\
        -j ${task.cpus} \\
        $input \\
        ${prefix}.${suffix} \\
        $args
"""

Feel free to get another reviewer here, but otherwise you can't capture the dupes file unless you simplify your existing output by removing the suffix, but then you have to deal with a tuple[meta, file, file] in the workflow.

[DLBPointon]

pbmarkdup can take a list of files as input, so i think you may just need to do some double checks to make sure names don't conflict.

Make sure input and output file names don't conflict, which seems like it could happen.

Adapted from CAT_CAT

    if(file_list.contains("${prefix}.{suffix}") {
        error "PBMARKDUP: The name of the input file can't be the same as the output: " +
        "Change the prefix to avoid conflict."
    }

As it can take a list of input files, perhaps a check to make sure they are in fact unique files too? However i think this can be optional as it should be checked in the input_check or workflow of the pipeline.

    def input_files = [input].collect { file.baseName }
    if (input_files.size() != input_files.unique().size()) {
        error "PBMARKDUP: Input files must have unique names. Found duplicates: ${input_files}" +
        "Check your input reads"
    }

[sainsachiko]

Thanks @DLBPointon for kindly reviewing this. I have updated the code regarding your reviews, please take a look, thank you!