Alignment workflow

[rlancaster96]

config file must be updated defining what containers to run for each process like this:

singularity {
    enabled = true
    autoMounts = true
    cacheDir = '/path/to/cache/singularity'
    }

// Define containers for each process
process {
    withName:FastQC {
        container = '/path/to/file/fastqc.sif'
    }

    withName:TrimmomaticPE {
        container = '/path/to/file/trimmomatic.sif'
    }
}