Updates to Monopogen to work with new versions of samtools + bcftools

[swvanderlaan]

Thanks for the nice tools. I have been tinkering with it to be able to use the new versions of samtools and bcftools.

I believe this should be correct - but is depending on a proper comparison of the original output. See this issue.

• Updated Monopogen to work with new versions of samtools and bcftools which are system installed through for instance conda (more generic) or brew (macOS).
• Added --verbose flag to all sub-processes.
• Edited mkdir and check existing tools functions.

I also created a flow to install Monopogen:

• Install your favorite condo, I used miniconda3.
• Create a new environment: conda create --name monopogen "python=3.8"; follow instructions (if any).
• Activate the new environment: conda activate monopogen.
• Make sure the monopogen-environment includes the right versions of these tools: pip install "pandas>=1.2.3" "pysam>=0.16.0.1" "NumPy>=1.19.5" "sciPy>=1.6.3" "pillow>=8.2.0"