specify available memory to Picard about methylseq

[ewels]

Hi @zchatt,

Thanks for your detailed issue and fix! Yes, I think we should be specifying the memory available for Picard. We're already doing this in other nf-core pipelines, so it should be a simple fix:

    script:
    if( !task.memory ){
        log.info "[Picard MarkDuplicates] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this."
        avail_mem = 3
    } else {
        avail_mem = task.memory.toGiga()
    }
    """
    picard -Xmx${avail_mem}g MarkDuplicates \\

Phil

[ewels]

Hi @zchatt,

I've just made this change and merged into the dev branch. You can use this code by specifying -r dev when running nextflow. Hopefully this will solve your problem.

It'll be properly released when the next version of the pipeline goes out.

Let us know if you hit any problems and thanks for reporting this!

Phil

[zchatt]

Fantastic. I will give it a go now. Cheers, Z