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config_sim_data.yaml
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config_sim_data.yaml
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####################
#### SOFTWARE
elai: "/shared/projects/vietcaf/scripts/elai/elai-lin" # "/data3/projects/vietcaf/baotram/scripts/robusta_vn/elai/elai-lin"
vcftools: "vcftools/0.1.16"
singularity: "/shared/projects/vietcaf/scripts/snakelai/singularity-container_myr_4-0-2_rstudio_1.3.sif"
####################
#### INPUT FILES
genome: "/shared/projects/vietcaf/data/reference/CC1.8_v2_pseudomolecule_cat.fa" # reference, only used if run "snakemake merge_elai"
source_files: [
"/shared/projects/elai_most/benchmark_elai/input/group_AG",
"/shared/projects/elai_most/benchmark_elai/input/group_C",
"/shared/projects/elai_most/benchmark_elai/input/group_D",
"/shared/projects/elai_most/benchmark_elai/input/group_ER",
"/shared/projects/elai_most/benchmark_elai/input/group_OB"
] # if simulate_source = FALSE, provide genotype file for each source
test_file: "/shared/projects/elai_most/benchmark_elai/input/test_hybrid345" # if filled, test_id will be ignored
snp_file: "/shared/projects/elai_most/benchmark_elai/input/snp.pos_1" # obligator if test_file is provided, columns: id, pos, chrom
source_vcf: ""
test_vcf: ""
test_id: [] # "@" for all genotypes or specific id
chromosome: [1] # "@" for all chromosome or specific chroms
####################
#### OUTPUT
outdir: "/shared/projects/elai_most/benchmark_elai/snakelai_output"
######################
#### SNP SELECTION
# random_snps: true # random or ordered
# n_batches: 1 # only if "random" split
# batch_size: 1000 # number of snps per batch
# snp_den: [1, 500000] # random selection only, snp density: [nb snps, per kb]. if this object is set, batch_size will be ignored
split_snps_cores: 20
snp_selection:
10k: # select random 10k snps in the chromosome
nb_snps: 10000
window_size: "chrom"
100k: # select random 100k snps in the chromosome
nb_snps: 100000
window_size: "chrom"
even: # select 1 snp per non-overlapping windows of 5000 bp
nb_snps: 1
window_size: 5000
all: # use all the snps provided, but plit them into chunks of 100k snps
nb_snps: "all"
window_size: 100000
# nb_batches: 1 # number of snp sets to be randomly selected
######################
#### SOURCE GENOTYPES SIMULATION
simulate_source: FALSE # TRUE or FALSE
nb_groups: 5 # nb of source populations
nb_genotypes: 100 # nb of genotypes per group, only effective if simulate_source = TRUE
simulate_cores: 10 # nb of cores for simulation, only effective if simulate_source = TRUE
simulate_mem_gb: 10 # nb of mem usage for simulation, only effective if simulate_source = TRUE
####################
#### ELAI PARAMS
# elai_source: "/data3/projects/vietcaf/baotram/scripts/robusta_vn/elai/elai-lin"
elai_params:
c5_mg5: "-c 5 -mixgen 5 --exclude-nopos --exclude-miss1"
c5_mg10: "-c 5 -mixgen 10 --exclude-nopos --exclude-miss1"
c5_mg20: "-c 5 -mixgen 20 --exclude-nopos --exclude-miss1"
c5_mg30: "-c 5 -mixgen 30 --exclude-nopos --exclude-miss1"
c15_mg5: "-c 15 -mixgen 5 --exclude-nopos --exclude-miss1"
c15_mg10: "-c 15 -mixgen 10 --exclude-nopos --exclude-miss1"
c15_mg20: "-c 15 -mixgen 20 --exclude-nopos --exclude-miss1"
c15_mg30: "-c 15 -mixgen 30 --exclude-nopos --exclude-miss1"
c25_mg5: "-c 25 -mixgen 5 --exclude-nopos --exclude-miss1"
c25_mg10: "-c 25 -mixgen 10 --exclude-nopos --exclude-miss1"
c25_mg20: "-c 25 -mixgen 20 --exclude-nopos --exclude-miss1"
c25_mg30: "-c 25 -mixgen 30 --exclude-nopos --exclude-miss1"
#c5_mg10_s60: "-c 5 -mixgen 10 -s 60 --exclude-nopos --exclude-miss1"
elai_mem_gb: 15 # mem in Gb for each ELAI run
#######################
#### MERGE ELAI RESULTS
# only works if run "snakemake merge_elai"
merged_snps: ["even", "all"]
merged_params: "c5_mg_20"