Sporothrix-annotation/nextflow.config at main · SJ-31/Sporothrix-annotation · GitHub

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conda.enabled = true
executor {
    name = "local"
    queueSize = 5 // Controls how many processes will run in parallel, setting this too high is not advised if you are not using a computer cluster
}
includeConfig 'config/controller.config'
includeConfig 'config/paths.config'

params.spadesargs = "" // Arguments for spade assembler
params.bbduk_args = 'k=31 -Xmx1G -Xms16M' // Arguments passed for BBDuk
params.ontologizer_jar = "/home/sc31/Bio_SDD/tools/Ontologizer.jar" // The path to the Ontologizer jar file
params.readgroups = "RGID=1 RGLB=lib1 RGPL=ILLUMINA RGPU=unit1 RGSM=2" // Arbitrary read groups that are necessary to assign in order to use GATK software

// Maker configuration
    // First round of annotation
params.genemarks = "$projectDir/results/annotation/genemarks_hmms"
params.makerR1 = ["opts_est2genome=1 opts_protein2genome=1 opts_protein=$params.prot opts_est=$params.est opts_model_org= opts_rmlib=$params.rep_lib opts_repeat_protein=$rep_prot opts_altest_gff=$params.ref_gff",
    "$params.genemarks"]

    // Second round of annotation
params.makerR2 = 'opts_est_pass=1 opts_altest_pass=1 opts_protein_pass=1 opts_rm_pass=1 opts_model_pass=1 opts_pred_pass=1 opts_other_pass=1 opts_est2genome=0 opts_protein2genome=0 opts_model_org= opts_augustus_species=Sporothrix_schenckii'

    // Third round of annotation
params.makerR3 = 'opts_est_pass=1 opts_altest_pass=1 opts_protein_pass=1 opts_rm_pass=1 opts_model_pass=1 opts_pred_pass=1 opts_other_pass=1 opts_est2genome=0 opts_protein2genome=0 opts_model_org='