Reproducibility of conda environments

[rvosa]

The current version of the pipeline runs each step in an environment managed by conda. By first approximation, every rule has its own environment (in a few cases the environment can be shared by some rules), which consists of several bioinformatics tools and python packages. In all cases, the exact versions are not pinned, nor is the conda channel priority fixed. This means that the possibility exists that environments are not being reproduced precisely. In addition, these environments are being bootstrapped on the host machine, while SnakeMake allows for delegating this to a Docker container (which theoretically could be published in a container registry and reused). This issue is considered 'done' if a combination of the above enhancements is implemented such that the environments are guaranteed fully reproducible.