Updated README and folder structure

.gitignore

README.md

README_old.md

assembly/README.md

cluster/config.yaml

config/config.yaml

config/environment.yml

config/samples.tsv

container/README.md

container/assemblySC.def

container/conda-linux-64.lock

container/conda-lock.yml

container/environment.yml

notebooks/pangenome_graph.ipynb

resources/H37Rv.gbf

run_assembly_pipeline.py

variantcalling/README.md

variantcalling/config/biopython.yaml

variantcalling/config/config.yaml

variantcalling/config/samples.txt