MOLGENIS pipelines

Pipelines

This repository contains the following pipelines:

• Imputation
• RNA-seq (Experimental)

It also contains pipelines with their own repo's like:

• NGS_DNA
• NGS_RNA

In addition it contains protocols that may be re-used between different (versions of a) pipeline(s).

How to get started

Below we explain (step 1) how to download and deploy Molgenis Compute. This distribution already contains several pipelines/protocols/parameter files which you can use 'out-of-the-box' to align and impute your NGS data. Next, we explain (step 2) how you can download even more pipelines and protocols by cloning this repo.

For a 'walkthrough' tutorial on Molgenis Compute, please go here

Step 1: download Molgenis Compute

• Download the latest MOLGENIS Compute from https://github.com/molgenis/molgenis-compute/releases

• Currently (April 2017) MOLGENIS Compute v1.4 (16.11.1)

create dir

mkdir mycompute
cd mycompute

download

wget https://github.com/molgenis/molgenis-compute/releases/download/v16.11.1/molgenis-compute-v16.11.1.tar.gz
tar -xzvf molgenis-compute-v16.11.1.tar.gz

test

sh molgenis_compute.sh

Step 2: clone this repo

For read/write access:

git clone https://github.com/molgenis/molgenis-pipelines.git

Table of Contents

• Release Notes

• Environment setup with easybuild

  • Install environment

• NGS_DNA

• NGS_RNA

  • Install pipeline
  • Dependencies
  • Run
  • Workflow
  • Protocols)

• MOLGENIS Compute

  • Quickstart
  • Parameters
  • Reference
  • Read more

• MOLGENIS CoNVaDING

  • CoNVaDING