proposed production-level config for humans

workflows/config/snakemake/production_config_HomSap.yml

@@ -0,0 +1,55 @@
+"population_id": [0] # (what is this a setting for?)
+
+# snakemake settings
+"seed": 12345
+"replicates": 3
+"output_dir": "results"
+
+# species-specific settings
+"species": "HomSap"
+"demo_models": [
+    {"id":"Constant", 
+    "num_samples_per_population": [100],
+    },
+    {"id":"OutOfAfrica_3G09",
+    "num_samples_per_population": [100,100,100],
+    }
+    {"id":"OutOfAfricaArchaicAdmixture_5R19",
+    "num_samples_per_population": [100,100,100],
+    }
+]
+"genetic_map": "HapMapII_GRCh37"
+"chrm_list": "chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21"
+"dfe_list": ["none", "Gamma_H17"]
+"annotation_list": ["all_sites", "ensembl_havana_104_exons"]
+"mask_file": "workflows/masks/HapmapII_GRCh37.mask.bed"
+"stairway_annot_mask" : "" # set this or any of the below to 'none' to skip annot masking
+"msmc_annot_mask" : ""
+"gone_annot_mask" : ""
+"smcpp_annot_mask" : ""
+
+# slim settings
+"slim_scaling_factor": 1
+"slim_burn_in": 10
+
+# n(t) specific configs
+"methods" : ["stairwayplot", "gone", "smcpp", "msmc"]
+"num_sampled_genomes_msmc" : [6]
+"num_sampled_genomes_per_replicate": [2]
+"num_msmc_iterations" : 20
+"gone_phase" : 1  # 0 for pseudohaploid, 1 for phased, 2 for unknown phase
+"gone_max_snps" : 50000  # default=50000
+"gone_threads" : 8
+"gone_num_gens" : 2000  # default=2000
+"gone_num_bins" : 400  # default=400
+
+
+# exe paths
+"poly_dfe_exec": "ext/polyDFE/polyDFE-2.0-linux-64-bit"
+"dfe_alpha_exec": "ext/dfe-alpha-release-2.16/est_dfe"
+"dfe_alpha_data_path_1": "ext/dfe-alpha-release-2.16/data"
+"dfe_alpha_data_path_2": "three-epoch"
+"grapes_exec": "ext/grapes/multi_grapes"
+"msmc_exec" : "ext/msmc2/build/release/msmc2"
+"stairwayplot_code" : "ext/stairwayplot/swarmops.jar"
+"gone_code" : "ext/GONE/Linux"