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HPC Deployment toolbox used at WUR for Anunna

This repository contains a couple of scripts to make living with the WUR git repo a bit easier. Feel free to add code, by forking, coding and creating a merge request.

Basic definition files for containers

nemmap is a single-command pipeline to process bacterial (full 16S) or fungal (full ITS) reads obtained by Nanopore sequencing. This pipeline is developed and intended for internal use by the Laboratory of Nematology (WUR).

An automated pipeline to generate CADD scores.

Contains Instructions how to set up iRODS for sysadmins and training material for different user goups.

CNN methods that estimate the diameter of the crop, even when it's occluded.

Reliable CNV detection in plant genomes

NEmatology RNA Variant Analysis and Calling pipeline = NERVAC

Generate documentation pages using Markdown and MkDocs from a metadata excelsheet.