This repository aims to wrap a Snakemake pipeline for generating QC metrics from sequencing data into Bionix, please refer to this repository for more about the pipeline. Some bioinformatics tools such as FastQScreen, Qualimap, Samtools_stats, and MultiQC that were used in the QC-pipe and yet to be available in BioNix's tools are wrapped.
The directory subread-wf is an example workflow that I started with, to utilise bioinformatics tools already available in BioNix.
The following are some notes regarding wrapping some of the particular tools.
FastQ-Screen always require a config file where an aligner and a list of databases should be specified, here we are using bowtie2.
This stage is specified solely through a flake. During this process, the FastQC was slightly redefined such that the output format is detectable by MultiQC
BioBloom is a tool that was not in the original QC pipeline. In my workflow, BioBloom is included to demonstrate that it can also be compiled in MultiQC's summary report.