;output dir
output_dir ./spades_output/

;history log (optional)
history_log quality.log

;contig storage (optional)
contig_storage ./spades_output/D.creature/dataset/

;data set name
name DATASET

;bulid agent (optional)
build_agent ANT01

;=== TOOLS PARAMETERS ===

;run prepare_cfg (optional, default true)
prepare_cfg true

;spades compile (optional, default true)
spades_compile true

;spades options, excluding output dir, disable gzip output,
;IMPORTANT! files have to be either specified by absolute path, either relatively to this config
spades_params "--sc --12 data.fastq"

;etalon saves, will add --debug to spades and compare saves faterwards (optional)
etalon_saves /data/etalon_saves

;quast options, excluding output (optional). ;
;will not assess contigs if not given
quast_params "-R genome.fasta -G genes.txt"

;QUAST dir
quast_dir /home/teamcity/quast-1.3/

;read quality options, excluding output (optional)
;will not assess reads if not given
reads_quality_params "-r genome.fasta"

;=== ASSESSING OPTIONS ===

;assess. will assess quast results ant/or reads quality (default false)
assess true

;min n50 (optional)
min_n50  10000

;max misassemblies (optional)
max_mis  2

;min genome mapped, % (optional)
min_genome_mapped  95.1

;min genes (optional)
min_genes  2400

;max indels (optional)
max_indels 10

;max mismatches (optional)
max_subs 10

;min reads aligned, % (optional)
min_aligned 64.4




