A simple pipeline to test some basic nextflow features.

Working through NextFlow tutorials. See https://github.com/nextflow-io/training

Bayesian phylogenetic analysis

Next-generation Sequencing workflows

An hello world pipeline to test nextflow installations.

Testing different pipelines using Nextflow

This directory contains material that I've used in different courses

A nextflow workflow to build referenceseeker DBs on the fly

Nextflow pipeline for targeted sequencing data.

My final thesis project work from my Biomedical Genomics MSc undertaken at NUIG, 2021. Includes Nextflow, Snakemake, Bash, Python and R scripts.

Advanced Training in Bioinformatics Workflows: Beginner - Intermediate level Bioinformaticians working with next-generation sequencing data in East-Africa.

Filter a VCF to discard false positive variants

A Nextflow pipeline for performing bacterial RNA-Seq analysis without a reference genome.

Nextflow pipeline encapsulating workflows for analyzing expansion lattice light-sheet microscopy (ExLLSM) imagery

HLA typing pipelines in nextflow

A nextflow pipeline for analysis and visualisation of NGS data using FastQC and Python Ploty Dash.

Nextflow pipeline to assemble genomes from long reads.

Nextflow Scripts/Workflows for Bioinformatics

EuroBioc2020 SPEAQeasy workshop https://eurobioc2020.bioconductor.org by Nick Eagles and Josh Stolz. For more information about SPEAQeasy check https://research.libd.org/SPEAQeasy/. For an example on how to use this RNA-seq processing pipeline and analyze the output files check https://research.libd.org/SPEAQeasy-example/.