nextflow.config

/*
 * -------------------------------------------------
 *  genome-annotation Nextflow config file
 * -------------------------------------------------
 * Default config options for all environments.
 * Cluster-specific config options should be saved
 * in the conf folder and imported under a profile
 * name here.
 */

process.container = "shub://ikmb-denbi/genome-annotation:latest"

/**********************
   Default parameters
 ***********************/

params { 
	proteins = false
	ESTs = false
	reads = false

	trinity = false
	pasa = false
	evm = false
	evm_weights = false

	augustus = false
	model = false
        augCfg = false
	utr = "off"

	funAnnot = true
	training = false

	rm_species = false
	rm_lib = false

	training = false
	training_models = 1000
	train_perc = 90
	train_set = false

	uniprot = ""

	chunk_size = 50000

	nblast = 100
	nexonerate = 100
	nchunks = 10 
	nevm = 10
	max_intron_size = 20000

	blast_options = "6 qseqid sseqid sstart send slen pident qlen qstart qend length mismatch gapopen evalue bitscore"

	blast_evalue = 0.00001
	blast_bitscore = 80

	singleEnd = false
	rnaseq_stranded = false
	outdir = "results"
	name = false
	help = false
	email = false
	plaintext_email = false

	run_name = "esga-annotation"

	pasa_mysql_user = false
	pasa_mysql_pass = false
	pasa_mysql_host = "localhost"
	pasa_mysql_port = 3306

	pri_prot = 5
	pri_est = 3
	pri_rnaseq = 4
}

/***************
   Profiles 
 ***************/
 
profiles {
	standard {
		includeConfig 'conf/ccga_medcluster.config'
		includeConfig 'conf/base.config'
	}
	ccga_fast {
                includeConfig 'conf/ccga_fast.config'
		includeConfig 'conf/base.config'
        }
	ikmb_dx {
		includeConfig 'conf/base.config'
                includeConfig 'conf/slurm_ikmbdx.config'
	}
	nbis {
		includeConfig 'conf/nbis_slurm.config'
		includeConfig 'conf/base.config'
	}

	assembly_cluster {
		includeConfig 'conf/slurm_assemblycluster.config'
		includeConfig 'conf/base.config'
	}
	custom_conda {
		includeConfig 'conf/base.config'
		includeConfig 'conf/conda.config'
		includeConfig 'conf/custom.config'
	}
	self_install {
		includeConfig 'conf/base.config'
		includeConfig 'conf/custom.config'
	}
	local {
		includeConfig 'conf/base.config'
	}
	none {
		// Don't load any config (for use with custom home configs)
	}
}


/***********************
    Pipeline Info
 **********************/
 
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']

timeline {
	enabled = true
	file = "${params.outdir}/pipeline_info/genome-annotation_timeline.html"
}
report {
	enabled = true
	file = "${params.outdir}/pipeline_info/genome-annotation_report.html"
}
trace {
	enabled = true
	file = "${params.outdir}/pipeline_info/genome-annotation_trace.txt"
}
dag {
	enabled = true
	file = "${params.outdir}/pipeline_info/genome-annotation_dag.svg"
}

manifest {
	homePage = 'https://github.com/ikmb-denbi/genome-annotation.git'
	description = 'This pipeline annotates an eukaryotic genome de novo with external hints.'
	mainScript = 'main.nf'
	version = '1.0'
	nextflowVersion = '18.12.0'
}

// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
  if(type == 'memory'){
    try {
      if(obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
        return params.max_memory as nextflow.util.MemoryUnit
      else
        return obj
    } catch (all) {
      println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
      return obj
    }
  } else if(type == 'time'){
    try {
      if(obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
        return params.max_time as nextflow.util.Duration
      else
        return obj
    } catch (all) {
      println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
      return obj
    }
  } else if(type == 'cpus'){
    try {
      return Math.min( obj, params.max_cpus as int )
    } catch (all) {
      println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
      return obj
    }
  }
}