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chrcc.yaml
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chrcc.yaml
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variables:
#level 0
seed: [1]
# level 1
community: !com
name: trial
profile: {mu: 0.1, sigma: 1}
clades:
- !clade
prefix: cladeProc
ancestor: test/ancestor.fa
donor: test/donor.fa
ntaxa: 5
tree: {algo: birth_death, birth_rate: 0.9, death_rate: 0.5}
- !clade
prefix: cladeDefined
ancestor: test/ancestor.fa
donor: test/donor.fa
ntaxa: 4
tree: {ref: 'file:test/trees/ladder.nwk'}
# level 2
alpha: [1, 0.5]
# level 3
xfold: [1, 2]
# level 4
num_3c: [5000, 10000]
options:
num_samples: 1
evo:
indel_freq: 1e-4
small_ht_freq: 1e-4
large_ht_freq: 1e-4
inversion_freq: 1e-4
wgs:
read_len: 150
insert_mean: 500
insert_sd: 100
ccc:
method: hic
enzyme: NlaIII
insert_mean: 500
insert_sd: 100
insert_max: 1000
read_len: 150
machine_profile: EmpMiSeq250
create_cids: true
output: out