README updates and some file shuffling

.gitignore

README.md

assembly/config/config.yaml

assembly/config/samples.tsv

assembly/container/README.md

assembly/container/assemblySC.def

assembly/container/conda-linux-64.lock

assembly/container/conda-lock.yml

assembly/container/environment.yml

assembly/resources/H37Rv.gbf

assembly/workflow/rules/annotate.smk

assembly/workflow/rules/assemble.smk

assembly/workflow/rules/circularize.smk

assembly/workflow/rules/common.smk

assembly/workflow/rules/readQC.smk

variantcalling/README.md

variantcalling/config/biopython.yaml

variantcalling/config/config.yaml

variantcalling/config/samples.txt

variantcalling/workflow/Snakefile