Config.ini

[Databases]
database_path: /project/j/jparkin/Lab_Databases
UniVec_Core: %(database_path)s/univec_core/UniVec_Core.fasta
Adapter: %(database_path)s/Trimmomatic_adapters/TruSeq3-PE-2.fa
Host: %(database_path)s/human_genome/human_genome.fasta
Rfam: %(database_path)s/Rfam/Rfam.cm
DNA_DB: %(database_path)s/choco_mpro_3/family_group
#DNA_DB: %(database_path)s/chocophlan_h3_chunks
#DNA_DB: /home/billy/choco_h3/choco_h3_group
#DNA_DB_Split: %(database_path)s/ChocoPhlAn/ChocoPhlAn_split/
Prot_DB: %(database_path)s/nr/nr
Prot_DB_reads: %(database_path)s/nr/nr
accession2taxid: %(database_path)s/accession2taxid/accession2taxid
nodes: %(database_path)s/WEVOTE_db/nodes_wevote.dmp
names: %(database_path)s/WEVOTE_db/names_wevote.dmp
Kaiju_db: %(database_path)s/kaiju_db/kaiju_db_nr.fmi
Centrifuge_db: %(database_path)s/centrifuge_db/nt
SWISS_PROT: %(database_path)s/swiss_prot_db/swiss_prot_db
SWISS_PROT_map: %(database_path)s/swiss_prot_db/SwissProt_EC_Mapping.tsv
PriamDB: %(database_path)s/PRIAM_db/
DetectDB: %(database_path)s/DETECTv2
WEVOTEDB: %(database_path)s/WEVOTE_db/
EC_pathway: %(database_path)s/EC_pathway/EC_pathway.txt
path_to_superpath: %(database_path)s/path_to_superpath/pathway_to_superpathway.csv
MetaGeneMark_model: /pipeline_tools/mgm/MetaGeneMark_v1.mod
taxid_tree: %(database_path)s/taxid_trees/class_tree.tsv
kraken2_db: %(database_path)s/kraken2
#[code]
#ga_pre_scan_get_libs = /home/billy/human_flu/30785/ga_pre_scan_get_libs.py


[Tools]
Python = python3
Java = java -jar
cdhit_dup = /pipeline_tools/cdhit_dup/cd-hit-dup
Timmomatic = /pipeline_tools/Trimmomatic/trimmomatic-0.36.jar
AdapterRemoval = /pipeline_tools/adapterremoval/AdapterRemoval
vsearch = /pipeline_tools/vsearch/vsearch
Flash = /pipeline_tools/FLASH/flash
BWA = /pipeline_tools/BWA/bwa
SAMTOOLS = /pipeline_tools/samtools/samtools
BLAT = /pipeline_tools/PBLAT/pblat
DIAMOND = /pipeline_tools/DIAMOND/diamond
Blastp = /pipeline_tools/BLAST_p/blastp
Barrnap = /pipeline_tools/Barrnap/bin/barrnap
#note: needle is quite slow.  This argument can be swapped for stretcher, but stretcher is not as accurate
Needle = /pipeline_tools/EMBOSS-6.6.0/emboss/needle
Blastdbcmd = /pipeline_tools/BLAST_p/blastdbcmd
Makeblastdb = /pipeline_tools/BLAST_p/makeblastdb
Infernal = /pipeline_tools/infernal/cmscan
Kaiju = /pipeline_tools/kaiju/kaiju
Centrifuge = /pipeline_tools/centrifuge/centrifuge
Priam = /pipeline_tools/PRIAM_search/PRIAM_search.jar
Detect = /pipeline/Scripts/Detect_2.2.9.py
BLAST_dir = /pipeline_tools/BLAST_p
WEVOTE = /pipeline_tools/WEVOTE/WEVOTE
Spades = /pipeline_tools/SPAdes/bin/spades.py
MetaGeneMark = /pipeline_tools/mgm/gmhmmp

#default is 30, to coincide with cdhit_dup's default.  
[Settings]
AdapterRemoval_minlength = 30
#bypass_log_name = bypass_log_0.1.txt

Show_unclassified = No
RPKM_cutoff = 0.01
BWA_cigar_cutoff = 90
BLAT_identity_cutoff = 85
BLAT_length_cutoff = 0.65
BLAT_score_cutoff = 60
DIAMOND_identity_cutoff = 85
DIAMOND_length_cutoff = 0.65
DIAMOND_score_cutoff = 60

#determines how much memory should be free for use with each tool.  [1-99]
BWA_mem_threshold = 75
BLAT_mem_threshold = 75
DIAMOND_mem_threshold = 80
BWA_pp_mem_threshold = 30
BLAT_pp_mem_threshold = 75
DIAMOND_pp_mem_threshold = 80
DETECT_mem_threshold = 80
Infernal_mem_threshold = 75
Barrnap_mem_threshold = 75

#maximum allowable concurrent instances of the tool [1-number of cores on your machine]
BWA_job_limit = 40
BLAT_job_limit = 40
DIAMOND_job_limit = 40
BWA_pp_job_limit = 40
BLAT_pp_job_limit = 40
DIAMOND_pp_job_limit = 40
DETECT_job_limit = 40
Infernal_job_limit = 40
Barrnap_job_limit = 40

#determines how long (seconds) each job should wait before they are launched (imposes delay.  for memory-use-detection)
BWA_job_delay = 0.5
BLAT_job_delay = 5
DIAMOND_job_delay = 5
BWA_pp_job_delay = 0.01
BLAT_pp_job_delay = 0.05
DIAMOND_pp_job_delay = 5

#toggle these options to delete the interim data the steps will generate
keep_all = yes
keep_quality = no
keep_host = no
keep_vector = no
keep_rRNA = no
keep_repop = no
keep_assemble_contigs = yes
keep_GA_BWA = no
keep_GA_BLAT = no
keep_GA_DIAMOND = no
keep_GA_final = no
keep_TA = no
keep_EC = no
keep_outputs = no

#Data gets chunked in the pipeline.  Control the chunk size to reduece the number of files generated.  Increase for speed, and reduced memory load per tool-run [1-99999]
rRNA_chunk_size = 50000
GA_chunk_size = 10000
EC_chunk_size = 1000

#Decides the lossiness of host + vector filtration.  For paired-end annotation only.  [high/low] high: only if both pairs pass through the filter.  low: if either pair passes through filter, both pairs pass
filter_stringency = high

TA_mem_threshold = 80
TA_job_delay = 10


#[Labels]
#GA_BWA = test_GA_BWA_0.1
#GA_BLAT = test_GA_BLAT_0.1
r pair passes through filter, both pairs pass
filter_stringency = high

#[Labels]
#GA_BWA = test_GA_BWA_0.1
#GA_BLAT = test_GA_BLAT_0.1