default_configfile.yml

#Default config file for eukdetect. Copy and edit for analysis

#Directory where EukDetect output should be written
output_dir: "/path/to/dir"
  
#Indicate whether reads are paired (true) or single (false)
paired_end: true 

#filename excluding sample name. no need to edit if paired_end = false
fwd_suffix: "_R1.fastq.gz" 

#filename excludign sample name. no need to edit if paired_end = false
rev_suffix: "_R2.fastq.gz"

#file name excluding sample name. no need to edit if paired_end = true 
se_suffix: ".fastq.gz" 

#length of your reads. pre-trimming reads not recommended
readlen: 125

#full path to directory with raw fastq files
fq_dir: "/path/to/dir"

#full path to folder with eukdetect database files
database_dir: "/path/to/dir"

#name of database. Default is original genomes only database name
database_prefix: "ncbi_eukprot_met_arch_markers.fna"

#full path to eukdetect installation folder
eukdetect_dir: "/path/to/dir"

#list sample names here. fastqs must correspond to {samplename}{se_suffix} for SE reads or {samplename}{fwd_suffix} and {samplename}{rev_suffix} for PE
#each sample name should be preceded by 2 spaces and followed by a colon character
samples:
  sample1:
  sample2: