/*

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Nuclear Shotgun pipeline

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Default config options

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*/

manifest {

name = 'Nuclear Shotgun pipeline'

author = 'Kevin Nota and Benjamin Vernot'

homePage = ''

description = 'preprocessing and mapping reads to genomes'

nextflowVersion = '>=22.10'

version = 'v1.0'

}

cleanup = true

nextflow.enable.moduleBinaries = true

containerEngine = 'singularity'

singularity.enabled = true

process.executor = 'local'

profiles {

singularity {

singularity.enabled = true

singularity.autoMounts = true

}

}

params {

//main programs

build = false // building database

preprocessing = false // filter raw bam or fastq files

mapping = false // mappes the fastq files from the preproccing

//user flags

bams = "" // path to input bams

bams_tsv = "" // bam tsv

input_fastq = "" // path the the fastq file

input_fastq_tsv = "" // path to tsv with input fastqs

fastq_files = "filterd_fastq" // path the the fastq file //filtered for mapping

// output dir for all processes.

out_dir = "." // out_dir_path

// cluster_options

executor = 'sge' // sge/slurm/local

memory = '8'

memory_max = '128 GB'

time = ''

time_max = '24h'

// hard coded, should be changed for external

path_reference_dbs = "/mnt/sequencedb/bowtie2_RefSeq/800_ncbi_genomes/" // path to bowtie2 indexes

//preprocessing flags

min_read_length = 35 // minimal read length

max_low_complexity_bases = 10 // max number of low complexity bases

//build flags

refgenomes = false

sink = false

// databases

all = false

vertebrate = false

plant = false

invertebrate = false

vertebrate_mammalian = false

vertebrate_other = false

bacteria = false

sinks = false

bact_sink = false

fungi_sink = false

archaea_sink = false

//process settings

threads = 8 // 8 cores default

maxForks = 5 // number of parallel local jobs

maxForks_cluster = 10 // number of parallel cluster jobs (suggesting to run 100 for increased speed)

}