reads2filterdAssembly.conf

singularity.enabled = true
singularity.autoMounts = true
executor.perJobMemLimit = true
condaEnv="/lustre/scratch123/tol/teams/blaxter/projects/tol-nemotodes/sw/miniconda3/envs/btk_env"
rCondaEnv="/lustre/scratch123/tol/teams/blaxter/projects/tol-nemotodes/sw/miniconda3/envs/nemaChromQC"
kmerContainer="/lustre/scratch116/tol/projects/tol-nemotodes/sw/.singularity/genokmer_0.1.sif"
buscoContainer="/nfs/users/nfs_p/pg17/busco_v4.1.2_cv1.sif"

process{
    memory = '3 GB'
    withLabel: big_parallelizable {
        errorStrategy = { task.attempt == 1 ? 'retry' : 'ignore'}
        maxRetries = 2
        queue = { task.attempt > 1 ? 'long' : 'normal' }
	}
    withName: map_reads {
   	    cpus = 24
   	    memory = '20 GB'
	}
    withName: 'kmer_hist|kat_plot' {
   	    cpus = 10
   	    memory = '25 GB'
	}
    withName: diamond_search {
   	    cpus = 8
   	    memory = '10 GB'
	}
    withName: hifiasm {
   	    cpus = 18
   	    memory = '40 GB'
	}
    withName: busco {
   	    container = "$buscoContainer"
        cpus = 12
   	    memory = '25 GB'
	}
    withLabel: kmer {
        container = "$kmerContainer"
	}
    withLabel: btk {
        conda = "$condaEnv"
	}
    withLabel: r {
        conda = "$rCondaEnv"
	}
}


profiles {
    standard {
        process.executor = 'local'
    }
    farm {
        process.executor = 'lsf'
        executor.perJobMemLimit = true
    }
}