Feature request: add support for specifying samples directly

[Redmar-van-den-Berg]

Describe the bug Currently, quac expects a certain directory structure to identify samples and bam/vcf files, which makes it difficult to use with existing pipelines, which may have a different folder structure. It would be nice to have a way to explicitly specify samples and files, so that users do not have to replicate the exact folder structure that quac expects.

Additional context One way to do this would be to add support for something like PEP, which can be as simple as a csv file, but also supports more complex project configurations. Snakemake already has native support for PEP, see here, so this should not be difficult to add to quac.

[ManavalanG]

Changes will be made in several stages:

• [x] 1. Refactor for WGS mode in minimal manner (w/o --include_prior_qc, --allow_sample_renaming) - #87
• [x] 2. Refactor for Exome mode in minimal manner (w/o --include_prior_qc, --allow_sample_renaming) - #88
• [x] 3. Refactor to allow --include_prior_qc - #89
• [x] 4. Refactor to allow --allow_sample_renaming - #89

[ManavalanG]

@Redmar-van-den-Berg We have now implemented the requested change. Users can now provide input info in a config file via --sample_config. Documentation is available here (please be sure to use the latest version in readthedocs at the bottom right).