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config.yaml
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#source_genotypes: ["/data3/projects/vietcaf/baotram/scripts/robusta_vn/elai/snakemake/input/group_AG", "/data3/projects/vietcaf/baotram/scripts/robusta_vn/elai/snakemake/input/group_C", "/data3/projects/vietcaf/baotram/scripts/robusta_vn/elai/snakemake/input/group_D", "/data3/projects/vietcaf/baotram/scripts/robusta_vn/elai/snakemake/input/group_ER", "/data3/projects/vietcaf/baotram/scripts/robusta_vn/elai/snakemake/input/group_OB"]
####################
#### SOFTWARE
elai: "elai/elai-lin" # "/data3/projects/vietcaf/baotram/scripts/robusta_vn/elai/elai-lin"
vcftools: "vcftools"
singularity: "shub://vibaotram/singularity-container:myr_4-0-2_rstudio_1.3.sif"
####################
#### INPUT FILES
# source_genotypes: ["/data3/projects/vietcaf/baotram/scripts/robusta_vn/elai/snakemake/input/group_AG", "/data3/projects/vietcaf/baotram/scripts/robusta_vn/elai/snakemake/input/group_ER"]
# test_genotype: "/data3/projects/vietcaf/baotram/scripts/robusta_vn/elai/snakemake/input/test_hybrid"
# snp_file: "/data3/projects/vietcaf/baotram/scripts/robusta_vn/elai/snakemake/input/snp.pos"
genome: "/data3/projects/vietcaf/reference/CC1.8_v2_pseudomolecule_cat.fa" # fasta file
source_files: [] # if simulate_source = FALSE, provide genotype file for each source
vcf: "/data3/projects/vietcaf/baotram/vietcaf_general_DP_missing_indv_singletons_Filtered_biallelic.recode.vcf"
# source_vcf: "/data3/projects/vietcaf/baotram/vietcaf_general_DP_missing_indv_singletons_Filtered_biallelic.recode.vcf"
test_id: ["TR6m"] # "@" for all genotypes or specific id
test_file: "" # if filled, test_id will be ignored
snp_file: "" # obligator if test_file is provided, columns: id, pos, chrom
chromosome: [1, 2, 6] # "@" for all chromosome or specific chroms
####################
#### OUTPUT
outdir: "/data3/projects/vietcaf/baotram/scripts/robusta_vn/elai/snakemake/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:
nb_snps: 10000
window_size: "chrom"
100k:
nb_snps: 100000
window_size: "chrom"
even:
nb_snps: 1 # "all"/integer
window_size: 5000 # "chrom"/integer
all:
nb_snps: "all" # "all"/integer
window_size: 500000 # "chrom"/integer
# nb_batches: 1 # number of snp sets to be randomly selected
######################
#### SOURCE GENOTYPES SIMULATION
simulate_source: FALSE # TRUE or FALSE
nb_groups: 5
nb_genotypes: 100 # nb of genotypes per group
simulate_cores: 10
####################
#### ELAI PARAMS
# elai_source: "/data3/projects/vietcaf/baotram/scripts/robusta_vn/elai/elai-lin"
elai_params:
c5_mg20: "-c 5 -mixgen 20 --exclude-nopos --exclude-miss1"
#c5_mg10_s60: "-c 5 -mixgen 10 -s 60 --exclude-nopos --exclude-miss1"
elai_mem_gb: 5
merged_snps: ["even", "all"]
merged_params: "c5_mg_20"