# Defaults for PROT
# fixed
q_datatype=PROT
q_masker=SEGMASKER


# variables
q_rawfasta=
q_todo_label=
q_todo_file=
q_tree_enabled=0
q_tree_file=
q_tree_root=
q_orthodb_api="https://data.orthodb.org/current"
q_compress=0
q_aligner=DIAMOND
q_scheduler=${q_scheduler:=NONE}
q_select=CDHIT
q_cluster=BRHCLUS
q_impsource=""
q_impcopy=""
q_implink=""
q_exepath=${q_exepath="/usr/bin:/usr/local/bin:$HOME/bin"}
q_path_brhclus=${q_path_brhclus=""}
q_path_cdhit=${q_path_cdhit=""}
q_path_mmseqs=${q_path_mmseqs=""}
q_path_diamond=${q_path_diamond=""}
q_path_blast=${q_path_blast=""}
q_njobmax_batch=100
q_njobmax_local=0
q_alimatrix=1
q_nalignments=100
q_effdbsize=0
q_run_mode="DEFAULT"
q_overlap=30
q_selpid=97
q_maxeval=1.0e-3
q_pairscale=0.001


