config.yaml

# config for analysis

# most CPUs to ever use at once
max_cpus: 16

# amplicons sequenced by PacBio
amplicons: data/PacBio_amplicons.gb

# the primary target for which we are calling mutations
primary_target: SARS-CoV-2

# how to parse the amplicon
feature_parse_specs: data/feature_parse_specs.yaml

# do we get the sequencing data from the 'HutchServer' or 'SRA'?
seqdata_source: HutchServer

# list of PacBio sequencing runs linking barcodes to variants
pacbio_runs: data/PacBio_runs.csv

# list of Illumina sequencing runs of barcodes
barcode_runs: data/barcode_runs.csv

# output directories / files
summary_dir: results/summary
ccs_dir: results/ccs
process_ccs_dir: results/process_ccs
processed_ccs_file: results/process_ccs/processed_ccs.csv
variants_dir: results/variants
nt_variant_table_file: results/variants/nucleotide_variant_table.csv
codon_variant_table_file: results/variants/codon_variant_table.csv
counts_dir: results/counts
variant_counts_file: results/counts/variant_counts.csv
func_scores_dir: results/func_scores
func_scores_by_barcode_file: results/func_scores/func_scores_by_barcode.csv
func_scores_by_codon_substitutions_file: results/func_scores/func_scores_by_codon_substitutions.csv
func_scores_by_aa_substitutions_file: results/func_scores/func_scores_by_aa_substitutions.csv
figs_dir: results/figures
Titeseq_Kds_dir: results/binding_Kds
Titeseq_Kds_file: results/binding_Kds/binding_Kds.csv
Titeseq_Kds_homologs_file: results/binding_Kds/binding_Kds_homologs.csv
expression_sortseq_dir: results/expression_meanFs
expression_sortseq_file: results/expression_meanFs/expression_meanFs.csv
expression_sortseq_homologs_file: results/expression_meanFs/expression_meanFs_homologs.csv
global_epistasis_binding_dir: results/global_epistasis_binding
global_epistasis_binding_file: results/global_epistasis_binding/global_epistasis_binding_predictions.csv
global_epistasis_expr_dir: results/global_epistasis_expression
global_epistasis_expr_file: results/global_epistasis_expression/global_epistasis_expression_predictions.csv
single_mut_effects_dir: results/single_mut_effects
single_mut_effects_file: results/single_mut_effects/single_mut_effects.csv
homolog_effects_file: results/single_mut_effects/homolog_effects.csv
structure_function_dir: results/structure_function
dms_view_dir: results/dms_view
dms_view_file_RBD: results/dms_view/dms-view_table_RBD.csv
dms_view_file_spike: results/dms_view/dms-view_table_spike.csv
circulating_variants_dir: results/circulating_variants
antibody_epitopes_dir: results/antibody_epitopes
sarbecovirus_diversity_dir: results/sarbecovirus_diversity
logoplots_dir: results/logoplots
interactive_heatmap: docs/_includes/interactive_heatmap.html

# parameters for running PacBio `ccs` program
min_ccs_accuracy: 0.999
min_ccs_passes: 3
min_ccs_length: 50
max_ccs_length: 5000

# max error rate in gene / barcode CCSs retained for consensu building
max_error_rate: 0.0001

# Parameters for processing Illumina barcodes, assuming this structure:
#  [R2 binds] - [upstream] - [barcode] - [downstream] - [R1 binds]
#  This orientation is hard-wired in the barcode parser, but here it is opposite
#  Therefore, supplied the "downstream" sequence as reverse complemented upstream
# Passed to `dms_variants.illuminabarcodeparser.IlluminaBarcodeParser`:
illumina_barcode_parser_params:
  upstream: GCTCGCGGCCGC
  downstream: ''
  minq: 20
  upstream_mismatch: 1
  downstream_mismatch: 0