From VCFs to SNP distance matrix

Run Workflow in Galaxy

• Galaxy Main
• Galaxy France
• Galaxy Australia
• Galaxy Europe
• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Collection\nCollection of VCFs to analyze"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nReference genome of the MTBC ancestor"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Filter TB variants"];
  0 -->|output| 2;
  3["Generate the complete genome of each of the samples"];
  2 -->|output1| 3;
  1 -->|output| 3;
  ce5dd7a2-c33d-46b4-9f02-68c2bdfcf31a["Output\n#{input_file}"];
  3 --> ce5dd7a2-c33d-46b4-9f02-68c2bdfcf31a;
  style ce5dd7a2-c33d-46b4-9f02-68c2bdfcf31a stroke:#2c3143,stroke-width:4px;
  4["Concatenate genomes to build a MSA"];
  3 -->|output_file| 4;
  5["Keep only variable positions"];
  4 -->|out_file1| 5;
  6["Calculate SNP distances"];
  5 -->|output_fasta| 6;

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Importing into Galaxy

Hands-on: Importing a workflow

• Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
• Click on galaxy-upload Import at the top-right of the screen
• Provide your workflow
  • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
  • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
• Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/evolution/tutorials/mtb_transmission/workflows/main_workflow.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows