This lesson is still being designed and assembled (Pre-Alpha version)

Introduction to Workflows with Common Workflow Language: Setup

Software

These lessons are best followed using VSCode, and the Benten extension (which is a language server for CWL). We will also be using the CWL reference runner. Instructions for installing these are given below.

VSCode and Benten installation

Download and install VSCode.

Open VSCode and search for Benten in the marketplace. The name of the client extension is Rabix/benten. Follow the usual method to install the extension.

The VSCode Benten extension will require the Benten server to be installed too. It will prompt you to do this the first time you activate the extension.

CWL installation

To install the cwltool on Linux or Windows, follow these instructions.

Files

You will need to install some example files for this lesson. In this tutorial we will use RNA sequencing data.

Setting up a practice repository

For this tutorial some existing tools are needed to build the workflow. These existing tools will be imported via GitHub. First we need to create an empty git repository for all our files. To do this, use this command:

git init novice-tutorial-exercises

Next, we need to import bio-cwl-tools with this command:

git submodule add https://github.com/common-workflow-library/bio-cwl-tools.git

Downloading sample and reference data

Move inside the novice-tutorial-exercises directory and download the data:

mkdir rnaseq
cd rnaseq
wget --mirror --no-parent --no-host --cut-dirs=1 https://download.jutro.arvadosapi.com/c=9178fe1b80a08a422dbe02adfd439764+925/

Downloading or generating STAR index

To run the STAR tool index files generated from the reference files are needed. This is a large download (4 GB), so it is also possible to generate these files yourself.

Downloading

mkdir hg19-chr1-STAR-index
cd hg19-chr1-STAR-index
wget --mirror --no-parent --no-host --cut-dirs=1 https://download.jutro.arvadosapi.com/c=02a12ce9e2707610991bd29d38796b57+2912/

Generating

Create chr1-star-index.yaml in the the novice-tutorial-exercises directory:

InputFiles:
  - class: File
    location: rnaseq/reference_data/chr1.fa
	format: http://edamontology.org/format_1930
IndexName: 'hg19-chr1-STAR-index'
Gtf:
  class: File
  location: rnaseq/reference_data/chr1-hg19_genes.gtf
Overhang: 99

Generate the index files with cwltool:

cwltool bio-cwl-tools/STAR/STAR-Index.cwl chr1-star-index.yaml