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config.yaml
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# Specify sample names and read files
# tab-delimited table with three columns, see manual/usage.md
# sample_name read1_file [read2_file]
# if paired end, all samples must be paired end
# if single end, all samples must be single end
# is also outputted at the end of the preprocessing workflow as
# preprocessing/01_processing/classification_input.txt
sample_file: classification_input.txt
# output base directory - will contain subfolders for reports, plots, etc
outdir: kraken2_classification
read_length: 150 #or 100
taxonomic_level: 'S' # For bracken results. Probably dont need to chage. Options: D,P,C,O,F,G,S
# see database options below, or manual/databases.md
database: /labs/asbhatt/data/program_indices/kraken2/kraken_custom_jan2020/genbank_genome_chromosome_scaffold
############# Downstream processing #######################
# Do Bracken calculations and use it in downstream processing
run_bracken: True
# file defining sample groups. Tab delimited with two columns,
# see manual/downstream_plotting.md
# if empty string specified, all samples will be treated as one group
sample_groups_file: ''
###########################################################
########### Extracting unmapped reads #####################
# Can extract unmapped reads from this database for use with
# another database. Will be in output folder $outdir/unmapped_reads
extract_unmapped: False
###########################################################
########### database alternatives (see README): ###########
# Slow, but has sequenced genomes of all quality. Best classification results:
# /labs/asbhatt/data/program_indices/kraken2/kraken_custom_jan2020/genbank_genome_chromosome_scaffold
# Older version of the same database, used in many previous Bhatt lab analyses
# /labs/asbhatt/data/program_indices/kraken2/kraken_custom_feb2019/genbank_genome_chromosome_scaffold
# Fast, but only high quality genomes, misses some things:
# /labs/asbhatt/data/program_indices/kraken2/kraken_custom_oct2018/genbank_bacteria
# Viruses only:
# /labs/asbhatt/data/program_indices/kraken2/kraken_custom_feb2019/viral
# Viruses only, standard crassphage replaced with Guerin et. al genomes:
# /labs/asbhatt/data/program_indices/kraken2/kraken_custom_feb2019/viral_guerin_crassphage
###########################################################