Scripts/config/lambda.toml

version = 2
workspace_root = "../.."
publish = "files-only"

[defaults]
seed = 114514

[cases.illumina_se]
simulator = "dna"
[cases.illumina_se.parameters]
reference = "Lambda/reference/GCF_000840245.1_ViralProj14204_genomic.fna"
output_dir = "Lambda/wgs/illumina_se"
sample = "LAMBDA_SE"
technology_name = "illumina-se"
reads = 100
read_length = 100
fragment_mean = 300
fragment_sd = 30
long_read_mean = 3000
long_read_sd = 500
snvs = 5

[cases.illumina_pe]
simulator = "dna"
[cases.illumina_pe.parameters]
reference = "Lambda/reference/GCF_000840245.1_ViralProj14204_genomic.fna"
output_dir = "Lambda/wgs/illumina_pe"
sample = "LAMBDA_PE"
technology_name = "illumina-pe"
reads = 100
read_length = 100
fragment_mean = 300
fragment_sd = 30
long_read_mean = 3000
long_read_sd = 500
snvs = 5

[cases.pacbio_clr]
simulator = "dna"
[cases.pacbio_clr.parameters]
reference = "Lambda/reference/GCF_000840245.1_ViralProj14204_genomic.fna"
output_dir = "Lambda/wgs/pacbio_clr"
sample = "LAMBDA_CLR"
technology_name = "pacbio-clr"
reads = 25
read_length = 150
fragment_mean = 350
fragment_sd = 35
long_read_mean = 5000
long_read_sd = 1500
snvs = 5

[cases.pacbio_hifi]
simulator = "dna"
[cases.pacbio_hifi.parameters]
reference = "Lambda/reference/GCF_000840245.1_ViralProj14204_genomic.fna"
output_dir = "Lambda/wgs/pacbio_hifi"
sample = "LAMBDA_HIFI"
technology_name = "pacbio-hifi"
reads = 25
read_length = 150
fragment_mean = 350
fragment_sd = 35
long_read_mean = 5000
long_read_sd = 1000
snvs = 5

[cases.ont]
simulator = "dna"
[cases.ont.parameters]
reference = "Lambda/reference/GCF_000840245.1_ViralProj14204_genomic.fna"
output_dir = "Lambda/wgs/ont"
sample = "LAMBDA_ONT"
technology_name = "ont"
reads = 25
read_length = 150
fragment_mean = 350
fragment_sd = 35
long_read_mean = 5000
long_read_sd = 2000
snvs = 5