This is a demo about how to develop and deploy a pipeline using nextflow, scif, a container (Singularity and Docker) and its posterior deployment.
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Updated
Feb 25, 2019 - HTML
This is a demo about how to develop and deploy a pipeline using nextflow, scif, a container (Singularity and Docker) and its posterior deployment.
Atac-Seq pipeline
From QC to summary statistics
EuroBioc2020 SPEAQeasy workshop https://eurobioc2020.bioconductor.org by Nick Eagles and Josh Stolz. For more information about SPEAQeasy check http://research.libd.org/SPEAQeasy/. For an example on how to use this RNA-seq processing pipeline and analyze the output files check http://research.libd.org/SPEAQeasy-example/.
This directory contains material that I've used in different courses
Chip-Seq pipeline
A simple pipeline to test some basic nextflow features.
An hello world pipeline to test nextflow installations.
A repository with usage examples of various pipeline and workflow orchestration tools
My final thesis project work from my Biomedical Genomics MSc undertaken at NUIG, 2021. Includes Nextflow, Snakemake, Bash, Python and R scripts.
This repo contains pipeline implemented using the nextflow workflow management system for the analysis of genomics data
A nextflow pipeline for the analysis of 16S amplicon data built around RExMap
Filter a VCF to discard false positive variants
Testing different pipelines using Nextflow
Demultiplexing pipeline for sequencing data
Advanced Training in Bioinformatics Workflows: Beginner - Intermediate level Bioinformaticians working with next-generation sequencing data in East-Africa.
A Genome Annotation workflow for Eukaryotes
Scripts for ARIBA-based gene detection
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