Welcome to the central config repository of my little pipeline ecosystem. I am developing workflows for various applications in food safety monitoring, including taxonomic profiling of food stuff, assembly, annotation and profiling of bacterial isolates as well as the characterization of signatures of genetic modification in plant materials (seeds and processed products). And possibly more to come over the next months.
All pipelines are developed in Nextflow, using a common template with a focus on portability, high standard of implementation, ease of use and version control. I have previously developed within the nf-core project and most of the coding framework used here is based on conventions originally developed by nf-core for the Nextflow community. As such, nf-core developers will find it immediately familiar and users will appreciate the overall robustness.
I provide a detailed documentation with each pipeline (see below) as well as a general setup guide to prepare your system for running them. We have also collected answers to some common questions
Finally, here are instructions on how to actually set up your config file and contribute it.
The config files hosted here can be jointly used across the following pipelines:
GABI, short for 'genomic analysis of bacterial isolates' is a workflow for the assembly of bacterial genomes from quality-controlled read data and downstream characterization (annotation, MLST typing, etc). GABI supports short reads, Nanopore long reads as well as Pacbio HiFi reads.
FooDMe2 performs taxonomic profiling of mitochondrial amplicon data to detect and quantify eukaryote species from mixed samples. The main application is in detecting food fraud, such as mis-labelled ingredients or use of endangered animals in (processed) foods.