nextflow-to-notebook-workshop

Resources for the workshop "From Nextflow to Notebooks"

nextflow_assembly

nextflow_nonpareil

nextflow_sourmash

nextflow_variant_calling

nf-cloud-gpu-test

Simple test Nextflow pipeline for testing GPU capabilities with cloud systems such as AWS Batch

nf-core-atacseq

A modified version of the peer reviewed nf-core/atacseq analysis pipeline

nf-core-clinvap

nf-core-module-test

nf-fastq-dumper

Dump all fastqas from SRA project ID - just that

nf-gwas-pipeline

A Nextflow Genome-Wide Association Study (GWAS) Pipeline

nf-rnaseq-salmon

ngi-exoseq

This pipeline has moved! Please see:

normfigures

Scripts to preprocess entire GTEx dataset and produce all rough figures

notebooks-as-scripts-nf

omop-notebooks

onemetagenome

One metagenome pipeline to rule them all - this nextflow pipeline is a complete end-to-end metagenomic solution creating visualisations of taxonomic data from fastq input files, by utilising mmseq

open-targets-api-scripts

owen-biomarker-discovery-challenge-candidate-drugs

panelr

paramsa

Using uncertainty in multiple sequence alignments for phylogenetic trees and bootstrap support values

pathway-analysis

Nextflow pipeline to perfrom pathway analysis for RNASeq FASTQ files

patterns

A curated collection of Nextflow implementation patterns -- http://nextflow-io.github.io/patterns/index.html

pcgr

Personal Cancer Genome Reporter (PCGR)

pcgr-nf

Pipeline to run pcgr tool on vcf file

pgx-nf

Pharmacogenomics Nextflow pipeline for the BHKLAB to process the GRAY 2017 dataset

phenopolis

All Docker containers and files pertaining Phenopolis partnership

phenowrangle

Repository for phenotypic data wrangling pipelines and codebase

phesant

PHESANT - PHEnome Scan ANalysis Tool (pheWAS, Mendelian randomisation (MR)-pheWAS etc.) in UK Biobank

phewas

Performs a PheWAS analysis & generates a Manhattan plot using the PheWAS R package