Using existing workflows on Galaxy

In this step, you are going to learn how to import publicly available Galaxy workflows and execute them.

This workflow was edited from the original workflow available on Galaxy to include Nextstrain and Pangolin to assign lineage and clades. The workflow will run a series of tools to generate outputs such as: Consensus FASTA (SARS-CoV-2 assembled genome) MultiQC Report Clades and Lineages report Variant file (SNPs)

Here we used the COVID-19 ARTIC analysis protocol to analyse the FASTQ files already provided in step 1-17 Importing data onto Galaxy. To execute the workflow it is also required the bed file which contains the coordinates of the primers and the SARS-CoV-2 reference genome.

If you would like to follow the tutorial on your own, you will need the datasets available for download below. If you have already downloaded the dataset in step 1-17, you only need to download the BED file.

In the tutorial, we have explained only one of the outputs as there are multiple outputs produced. Now, have a look at those other outputs and see which of them are useful for further analysis and interpretations.

Read through the following questions, and discuss these with us and your colleagues in the comments:

• Did you know we can import publicly available workflows and execute them in Galaxy?
• Do you know any other workflow languages outside Galaxy? If so, which one do you think is easier to build and execute?
• Can you use any other workflows to analyse the same set of samples that you know of?