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config.yaml
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config.yaml
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#####################################################
# #
# parameters usually adjusted by the user each time #
# #
#####################################################
#
# workflow base directory
WFLOWDIR: "/home/lauber/workflows/01_VirusHunterGatherer"
#
# list with SRA accessions (empty string to use user-specified data)
ACCLIST: "/home/lauber/workflows/01_VirusHunterGatherer/3_examples/SRA_n3_acclist.txt"
#
# directory with fastq files
FASTQDIR: "/data/tests/SRA_n3_test"
#
# group of viruses to search for (RNAviruses, smallDNAviruses, largeDNAviruses)
VIRFAM: "RNAviruses"
#
# name of project folder
PROJECTID: "test_SRA_n3"
#
# number of threads to use for analysis of individual datasets
THREADS: 6
#
# assembler to be used for seed-based assembly using Genseed-HMM
ASSEMBLER: "cap3"
#
# flag to specify whether or not SRA data is to be analyzed
ISSRA: 1
#
# flag to enbable mapping against human genome; only recommended when analysing human samples
MAPHG38: 0
#
#####################################################
# #
# parameters usually adjusted by the user only once #
# #
#####################################################
#
# base directoy where results are saved
BASEDIR: "/data/virushunter"
#
# blast database used for 1st filtering step against contaminant sequences
DBFILTER: "/data/db/RefSeq/filter/filter"
#
# blast database used for 2nd filtering step against non-viral RefSeq
DBREFSEQ: "/data/db/RefSeq/refseq_protein/refseq_protein"
#
# blast database used for 3rd filtering step against viral RefSeq
DBVIRAL: "/data/db/RefSeq/viral_genomic/viral_genomic"
#
# list of viral accessions in RefSeq
ACCSVIRAL: "/data/db/RefSeq/viral_protein/viral_protein.acc_list"
#
# flag to enbable debugging mode
DEBUGMODE: 0
#
#
# flag to enable or disable filter against non-viral RefSeq protein database
ENABLE_FILTER_3: 0