Snakemake workflow to run ELAI with different parameters and SNP sets, and scripts to get average of multiple runs

Scripts here are adapted on IFB cluster. Branch 'itrop' is for scripts adapted on iTrop.

Run ELAI on simulated genotypes for testing (1 chromosome only)

Input

source files, test file, and snp file in ELAI input format containing all SNPs
define SNP sets

Here is my config file.

Steps

generate or spit SNP sets as predefined
run ELAI for each set of parameters and snp sets
evaluate the results by custom scripts

Here is my script to run Snakemake.

Run ELAI on real data (multiple chromosomes possibly)

Input

vcf file containing all the source individuals
vcf file containing all the test individuals
define SNP sets

Here is my config file.

Steps

spit the source and test genotypes by chromosomes
simulate source populations using the source individuals and generate source files for ELAI
generate test file for ELAI from the vcf file
generate or spit SNP sets as predefined
run ELAI for each set of parameters and snp sets
rerun ELAI by snakemake --forcerun elai
average results from ELAI runs by custom script
merge results from runs of different snp sets by custom script

Here is my script to run Snakemake.

Some notes

the workflow runs on singularity container: shub://vibaotram/singularity-container:myr_4-0-2_rstudio_1.3.sif
may need to change R lib path in the script files, and install all the packages before running to prevent failure of parallel jobs