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updated params for selection, fixed bugs, now computing stats with diploshic #108

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Dec 4, 2023
Merged

updated params for selection, fixed bugs, now computing stats with diploshic #108

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3 changes: 3 additions & 0 deletions environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,9 @@ dependencies:
- r-irkernel
- r-ggplot2
- r-dplyr
- r-patchwork
- r-scales
- r-ggnewscale
- libprotobuf=3.21.12
- pip:
- git+https://github.com/popsim-consortium/stdpopsim.git
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369 changes: 233 additions & 136 deletions power_analysis.ipynb
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2 changes: 1 addition & 1 deletion workflows/config/snakemake/oregon_profile_simple/config.yaml
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@@ -1,7 +1,7 @@
cluster:
mkdir -p logs/{rule} &&
sbatch
--partition=kern,kerngpu
--partition=kern,kerngpu,memory,memorylong,compute,computelong,preempt
--account=kernlab
--cpus-per-task={threads}
--mem={resources.mem_mb}
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4 changes: 2 additions & 2 deletions workflows/config/snakemake/sweep_config.yaml
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Expand Up @@ -18,7 +18,7 @@ demo_model:

# BGS configs
dfe_list:
- Gamma_H17
- Gamma_K17
annotation_list:
- ensembl_havana_104_exons

Expand All @@ -33,7 +33,7 @@ num_subwins: 10 # number of subwindows within focal to compute statistic
coeffs:
bounds: [0.03, 0.1]
grid_size: 1 # This will yield just one s=0.03 or 2Ns~600
sweep_min_freq: 0.8
sweep_min_freq: 0.95
time_multipliers: [1]

# slim settings
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