genomechronicler-sarek-nf

genomediver

Disease diagnosis using phenotypes and genotypes.

genomediverfilters

Genomic and Phenotypic filters for the Genome Diver project

genomic-packages

Centralised repo for genomics analyses related R packages

getdata

getfile

getvcf

gpus-nf

Minimal example to showcase use of GPU enabled machine with the google-lifesciences executor for Nextflow workflow

gwas

GWAS pipeline using SAIGE

gwas-rpackages-nf

gwas-sumstats-harmoniser

GWAS Summary Statistics Data Harmonisation

gwas-vcf-specification

Specification for the GWAS-VCF format (manuscript in preparation)

h3agwas

GWAS Pipeline for H3Africa

h3agwas-qc

QC workflow of h3agwas pipeline

hail-spark-test

hic

Analysis of Chromosome Conformation Capture data (Hi-C)

hipstr

hisat-stringtie

hisat2

Super simple HISAT2 mapping pipeline (used for FlowCraft component)

hla-la

Fast HLA type inference from whole-genome data

hlatyping

Precision HLA typing from next-generation sequencing data

htslib-s3-nf

An example nextflow for using s3 file in htslib tools without staging

https-download

Simple Nextflow pipeline to retrieve files from https links

images

Repository to store images/gifs to use as links in other repos/tutorials etc

imputation-comparison

Methods & scripts use to compare imputation pipelines, see https://blog.lifebit.ai/2019/05/30/what-is-the-best-imputation-pipeline/

individual-data-analysis

Nextflow pipeline for individual data analysis of cohort browser data

jax-jupyter

Jackson Labs hands-on workshop material for working in cloud Jupyter Notebook Sessions on CloudOS

jax-sci-nf

jax-tutorial

Tutorial for Jackson Labs intro to Nextflow, containers, FlowCraft and Deploit

jku78h87