Various edits related to the production run of the sweep pipeline.
Changes to the SLURM oregon profile to make Snakemake play nice with the huge load of sims
Increase in number of replicates per param (from 200 sims to 1000)
Update in diploSHIC (new Keras version)
Fixed a bug in diploSHIC training
Changed training params in diploSHIC so that the training is not too far from the simulated data (with stdpopsim) -- this can be diagnosed with the pca_sims_training.ipynb
Changes to resource usage in some rules
write_vcf part of the pipeline had to be adapted to deal with infinite sites assumption (bumping variants at 0 to position 1; removing variants that may happen at last position after rounding).
andrewkern
commented
1 month ago
Various edits related to the production run of the sweep pipeline.
write_vcfpart of the pipeline had to be adapted to deal with infinite sites assumption (bumping variants at 0 to position 1; removing variants that may happen at last position after rounding).