Welcome to Marple - Inherited Cancer pipeline 
https://github.com/clinical-genomics-uppsala/marple_rd_tc/
This pipeline is created to run on short-read Illumina data from a custom Twist Inherited Cancer panel, designed at Clinical Genomics Uppsala.
This snakemake pipeline uses the module system from Hydra Genetics to process .fastq.gz files. The pipeline produces a MultiQC .html report with QC-data, .bam alignment files, annotated .vcf.gz for SNVs and smaller indels, as well as .txt and .aed files for structural variants from Exomedepth. A genome.vcf.gz is also produced, but this is not normalized.
Marple uses the following hydra genetics modules:
Rulegraph
Marple - references pipeline
The repository also includes a workflow to create the normalpool needed for Exomedepth. The references pipeline is located in workflow/Snakefile_references and uses a specific units files units_references.tsv which need to include the path to a bam-file, preferably produced by Marple.
Marple - references pipeline only uses one Hydra Genetics module:
Rulegraph
Hydra-genetics
Hydra Genetics is an organization/community with the goal of making snakemake pipeline development easier, faster, a bit more structured and of higher quality.
We do this by providing snakemake modules that can be combined to create a complete analysis or included in already existing pipelines. All modules are subjected to extensive testing to make sure that new releases doesn't unexpectedly break existing pipeline or deviate from guidelines and best practices on how to write code.
There is also a small tutorial available to help you get started with Hydra-genetics.
Snakemake
Marple and Hydra-genetics are snakemake bases pipeline/tools. The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. Workflows are described via a human readable, Python based language. They can be seamlessly scaled to server, cluster, grid and cloud environments, without the need to modify the workflow definition. Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.
If Snakemake is new to you a good place to start is doing the snakemake tutorial since this will help you setting Marple up.