# Insert name of input files to run analysis
# All three input files used by the pipeline for one sample need to be given the same name, followed by the suffix .faa (amino acid, gene fasta file), .fna (nucleotide contig fasta file), .contig (table with contig and gene names).
# Only give name of files and not the suffix (.faa, .fna, .contig)
input_file: ["SAMPLE_A","SAMPLE_B"]

# Define unique name for your project
project: Project_A_PathoFact

# Define dir to files (wil also be the output directory
OUTDIR: /path/to/samples

# Define size of split fasta files (default 10 000 sequences/file)
size_fasta: 100000

# Workflow (default: "complete")
# complete: complete pipeline: toxin + virulence + (AMR + MGE) prediction
# Tox:      toxin prediction
# Vir:      virulence prediction
# AMR:      antimicrobial resistance (AMR) & mobile genetic element (MGE) prediction
workflow: "complete"

###########    
# SignalP #
###########
 
# Define path to signalP
signalp: "/path/to/signalp-4.1/signalp"

############
#   Toxin  #
############

# Define path to HMM
hmmscan_tool: "/path/to/hmmer-3.2.1/src/hmmsearch"
hmm_file: "databases/toxins/combined_Toxin.hmm"

#################
#    Virulence  #
#################

vir_hmm_file: "databases/virulence/Virulence_factor.hmm"

#############
#    AMR    #
#############
# Define path to deepARG
deep_ARG: "scripts/deeparg-ss/deepARG.py"

#Define path to Plasflow
Plasflow: "scripts/PlasFlow/PlasFlow.py"

# Define path to phage prediction tools
# Virsorter
virsorter: "scripts/VirSorter/wrapper_phage_contigs_sorter_iPlant.pl"
virsorter_data: "scripts/virsorter-data"

#VirFinder
DeepVirFinder: "submodules/DeepVirFinder/dvf.py"