Fix the environment

[JonasNilsson1]

This pull request modifies the Snakefile to load the conda environment for each step, and fixes some package conflicts. To run ITRAP, I first created a new environment using

conda create -n snakemake_env python=3.10
conda activate snakemake_env
conda install -c bioconda -c conda-forge snakemake=5.7.4

It was also necessary to add this line to my ~/.bashrc and ~/.zshrc:

export PATH="$HOME/miniconda3/bin:$PATH"

Then I could run the example with

conda activate snakemake_env
snakemake --config exp=exp13 run=run1 --use-conda