nextflow.config

// PRIMARY NEXTFLOW.CONFIG

// DEFAULT PARAMETERS
params {

	// BASIC PARAMS
	help = false
	version = false
	debug = false

	// INPUT/OUTPUT
	input = false
	output = "results"
	reference = false
	gff3 = false
	gtf = false
	proteins = false

	// GENERAL PARAMS
	run_all = false
	qc = true
	genmap = true
	skip_genmap = false
	assembly = true
	skip_assembly = false
	mapping = true
	snpcalling = true
	svcalling = true
	annotation = true

	// QC PARAMS
	run_fastqc = true
	run_trim = true
	run_pear = true

	// QC FASTQC PARAMS
	fastqc_threads = 24
	qc_fastqc_kmers = 7
	qc_fastqc_nogroup = false
	qc_fastqc_quiet = false

	// QC TRIM READS PARAMS
	trim_threads = 24
	qc_trim_adapter_file = "data/adapters/TruSeq3-PE-2.fa"
	qc_trim_use_adapter = true
	qc_clip_options = "2:30:10:2"
	qc_trim_options = "LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 AVGQUAL:20 MINLEN:50"

	// QC PEAR READS PARAMS
	pear_threads = 24
	qc_pear_options = "-p 0.01 -v 10 -m 999999 -n 50 -t 1 -q 0 -u 1 -g1 -s 2"

	// GENMAP PARAMS
	run_genmap = true
	genmap_threads = 24
	genmap_outputs = "-t -w -bg"
	genmap_kmers = 30
	genmap_errors = 2

	// ASSEMBLY PARAMS
	run_unicycler = true
	run_prokka = true

	// ASSEMBLY UNICYCLER PARAMS
	unicycler_threads = 24
	assembly_unicycler_mode = "normal"

	// ASSEMBLY PROKKA PARAMS
	prokka_threads = 24

	// MAPPING PARAMS
	run_breseq = true
	skip_breseq = false
	run_minimap2 = true
	skip_minimap2 = false
	run_bwa = true
	skip_bwa = false

	// MAPPING BRESEQ PARAMS
	breseq_threads = 24
	mapping_breseq_p = true
	mapping_breseq_options = "-m 30 -b 20"
	mapping_breseq_coverage = "--min-MQ 30 --min-BQ 20"

	// MAPPING MINIMAP2 PARAMS
	minimap2_threads = 24
	mapping_minimap2_options = "--sam-hit-only --secondary=yes -ax sr"
	mapping_minimap2_samblaster = true
	mapping_minimap2_coverage = "--min-MQ 30 --min-MQ 20"

	// MAPPING BWA PARAMS
	bwa_threads = 24
	mapping_bwa_options = "-M"
	mapping_bwa_samblaster = true
	mapping_bwa_coverage = "--min-MQ 30 --min-BQ 20"

	// SNPCALLING PARAMS
	run_freebayes = true
	skip_freebayes = false
	run_bcftools = true
	skip_bcftools = false
	run_lofreq = true
	skip_lofreq = false
	run_varscan = true
	skip_varscan = false
	run_mpileup = true
	skip_mpileup = false
	run_gdcompare = true
	skip_gdcompare = false

	// SNPCALLING FREEBAYES PARAMS
	freebayes_threads = 1
	snpcalling_freebayes_options = "--pooled-discrete --min-alternate-fraction 0.01 --min-alternate-count 5 --min-mapping-quality 30 --min-base-quality 20"
	snpcalling_freebayes_filter_options = "-f 'QUAL > 30'"

	// SNPCALLING BCFTOOLS PARAMS
	bcftools_threads = 1
	snpcalling_bcftools_mpileup_options = "-C 50 -q 30 -Q 20 -d 2000 -E -a FORMAT/AD,FORMAT/DP"
	snpcalling_bcftools_call_options = "-mAv -Ov"
	snpcalling_bcftools_varfilter_options = "-Q 10 -d 5 -D 2000"

	// SNPCALLING LOFREQ PARAMS
	lofreq_threads = 8
	snpcalling_lofreq_options = "-C 5 -d 2000 -m 30 -q 20 -Q 20 -D --call-indels"

	// SNPCALLING VARSCAN PARAMS
	varscan_threads = 8
	snpcalling_varscan_mpileup_options = "-C 50 -q 30 -Q 20 -d 2000 -E"
	snpcalling_varscan_snp_options = "--min-coverage 5 --min-avg-qual 20 --min-var-freq 0.01 --output-vcf 1"
	snpcalling_varscan_indel_options = "--min-coverage 5 --min-avg-qual 20 --min-var-freq 0.01 --output-vcf 1"

	// SNPCALLING MPILEUP PARAMS
	mpileup_threads = 1
	snpcalling_mpileup_options = "-C 50 -q 30 -Q 20 -d 2000 -E"

	// SNPCALLING GDCOMPARE PARAMS
	gdtools_threads = 1

	// SVCALLING PARAMS
	run_pindel = true
	skip_pindel = false
	run_gridss = true
	skip_gridss = false

	// SVCALLING PINDEL PARAMS
	pindel_threads = 8
	svcalling_pindel_sam2pindel_options = "300 tag 0 Illumina-PairEnd"
	svcalling_pindel_options = "-c ALL"

	// SVCALLING GRIDSS PARAMS
	gridss_threads = 8
	svcalling_gridss_options = "-C 5 -d 2000 -m 20 -q 5 -Q 5 -D --call-indels"

	// ANNOTATION PARAMS
	run_snpeff = true
	skip_snpeff = false

	// ANNOTATION SNPEFF PARAMS
	snpeff_threads = 1
	annotation_snpeff_type = "gff3"
	annotation_reference_name = "refname"
	annotation_reference_version = "0.0"
	annotation_reference_codon_table = "Bacterial_and_Plant_Plastid"
	annotation_snpeff_config_file = "data/snpEff.config"

}

// NEXTFLOW PROFILES
profiles{
	// -profile cluster
	cluster {
		executor {
			name = 'slurm'
			queueSize = 200
			pollInterval = '30 sec'
		}
		process{
			executer = 'slurm'
			cpus = 16
			queue = 'standard'
			time = '12h'
			memory = '64 GB'
		}
	}
}

// Defaults only, expecting to be overwritten
params {
	max_memory = 250.GB
	max_cpus = 24
	max_time = 48.h
}

// NEXTFLOW MANIFEST
manifest {
	homePage = "https://gitlab.gwdg.de/mpievolbio-it/snpless-nf"
	author = "Kristian Ullrich"
	description = "A Nextflow pipeline for time-course analysis with NGS whole-genome data."
	mainScript = "main.nf"
	version = "0.1"
	nextflowVersion = ">= 21.00.0"
}

// NEXTFLOW REPORTING
dag {
	enabled = true
	file = "${params.output}/dag.svg"
}
report {
	enabled = true
	file = "${params.output}/report.html"
}
timeline {
	enabled = true
	file = "${params.output}/timeline.html"
}
trace {
	enabled = true
	file = "${params.output}/trace.txt"
}