1.9

• Refactors QuaC to add native support to QC fastq files using FastQC and Fastq Screen.
  • FastQC and Fastq Screen commands used are based on those in the small_variant_caller_pipeline. Tool versions were
    upgraded and switched from container+conda env to container-only set up.
• Rule multiqc_rename_config was brought in as well from the small_variant_caller_pipeline.
• --include_prior_qc is still used but only for Picard markduplicates.
• Updates conda env to run quac. Switched from snakemake-minimal to full snakemake for pandas.
• Updates input data set up and configs for system testing.
• Updates docs.

What's Changed

• Refactors to natively run QC on FASTQ files by @ManavalanG in #100

Full Changelog: 1.8...1.9