config.yaml

### Resources GB, min

build_mem : 100
build_time: 300

kraken_threads : 8
classify_time: 15 # kraken is quite fast [min]
braken_threads: 10

### store one or several name : path
# 'human' and 'mouse' can automatically be downloaded
kraken_db:
  db_name : "path/kreken_db"


#### Mapping

paired_reads: true

classify_db: 'default'  # If 'default' take first from 'kraken_db' pats above

classify_level:
  - species
#  - genus

sample_table: "samples.tsv"
## braken needs to know readlength approximatively utually databases for 50,100, and 150 are available
readlength: "infer_one"  # int , 'infer_one' if readlength is expected to be the same for all samples or 'infer_all'


kraken_run_extra: "--gzip-compressed "



### Build
build_db_name : "kraken_db"
taxonomy: "green_genes_taxonomy.tsv"
genome_folder: /home/kiesers/s/HumanUnifiedCatalog/gff/fasta