CW22 CWL Novice Template

CWL Template for the Collaborations Workshop 2022 CWL Tutorial.

This template contains scripts for use in the tutorial. It also contains instructions for installing the bio-cwl-tools library.

Before following the tutorial you should follow the software installation instructions in the CWL Tutorial Setup page.

Setup Instructions

This repository template can be used to create a new git repository, for you to store the scripts that you create during the tutorial for later reference. The steps for doing this
are listed below. The --recursive flag is used when cloning the repository locally, which will automatically load the bio-cwl-tools library too, using git submodules.

1. Creating your own github repository

Click the Use this template button, and create a new repository on github as you would usually.

2. Clone the repository locally

Clone the repository locally, using git clone --recursive [template address] (the [template address] can be got from the Code button at the top of the page).

3. Downloading input files

The required input files can be downloaded by running bash download_inputs.sh. This will create the directory rnaseq, and download the files GSM461177_1_subsampled.fastqsanger and GSM461177_2_subsampled.fastqsanger. Note that these files are each 136Mb large, so will take a few minutes to download, depending on your internet connection speed.

Workshop Instructions

There are two workflows in the repository, 1_Single_step_workflow.cwl and 2_Multi_step_workflow.cwl. These can be run using the commands:

1. cwltool 1_Single_step_workflow.cwl workflow_input.yml
2. cwltool 2_Multi_step_workflow.cwl workflow_input.yml

The scripts need to be completed before being run - replace the blocks indicated by < > with the appropriate code. Working examples of these scripts are provided in the CWL_Script_Solutions directory (note that you will have to copy these to the base directory to run though, so that the tool paths are correct).