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config.yaml
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config.yaml
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# Pipeline Configuration
# Flag to indicate which platform the data was sequenced on
# SEQUENCING_PLATFORM must be either RS2 or SEQUEL
SEQUENCING_PLATFORM: RS2
# Path to the folders which contain the sequencing output for each cell
SOURCE_DATA_PATHS:
- /path/to/cell_1/raw/data
- /path/to/cell_2/raw/data
- /path/to/cell_n/raw/data
# Path to barcode fasta file used for demultiplexing
BARCODES: /path/to/barcodes.fasta
# Path to the genome fasta file to be used for mapping/alignment
# The location of this file should be writable so that indexes can be created
GENOME: /path/to/genome.fasta
# Path to the ensembl annotation file for the genome
ANNOTATIONS: /path/to/ensembl/annotations.gtf
# path to the gene definition file(s)
LOCI:
- /path/to/locus/definition/file
# params for individual stages
# to disable a stage, remove its parameters
STAGE_PARAMS:
CCS:
minLength: 1000
maxLength: 10000
minPasses: 1
minPredictedAccuracy: 0.75
numThreads: 2
LIMA:
same: True # symmetric barcoding
num-threads: 4 # number of threads
dump-clips: True # save the clipped adapters
CCS_AMPLICON:
min-ccs-length: 6000
max-ccs-length: 7000
min-ccs-passes: 1
min-ccs-qual: 0.95
max-homopolymer: 2
trim-ends: 0
tsne-iterations: 5000
tsne-rate: 50
cluster-percentile: 10
cluster-inflation: 1.4
cluster-size-threshold: 0.2
max-cluster-size: 300
consensus-fraction: 0.25
min-haplotype-molecules: 10
min-variant-qual: 50
max-phasing-seqs: 100
forward-primer: GCAGTCGAACATGTAGCTGACTCAGGTCACATGGCAGCTGCCATACAATCCACCTG
reverse-primer: TGGATCACTTGTGCAAGCATCACATCGTAGCGACTGAGCCCTGGGAGGTAGGTAG
max-primer-dist: 5
HAPLOTYPER:
# ignore variants at start/end of sequence when determining haplotypes
ignoreBoundary: True
VARIANT_EFFECT:
# The location of the folder containing cache files for use by vep
vep_cache_dir: /exports/genomes/species/H.sapiens/GRCh38/annotation/vep/88
# The version of the cache to be used
vep_cache_version: 88
# ignore variants at start/end of sequence?
ignoreBoundary: True