From VCFs to SNP distance matrix

evolution-mtb_transmission/main-workflow

Author(s)

Version
1
Last updated
Mar 16, 2022
License
None Specified, defaults to CC-BY-4.0
Tags
evolution

Features
Tutorial
Identifying tuberculosis transmission links: from SNPs to transmission clusters
Other workflows associated with this material
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00076
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
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;

Inputs

Input Label
Input dataset collection Collection of VCFs to analyze
Input dataset Reference genome of the MTBC ancestor

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.1.3+galaxy0 TB Variant Filter Filter TB variants
toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.9+galaxy2 bcftools consensus Generate the complete genome of each of the samples
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1 Concatenate datasets Concatenate genomes to build a MSA
toolshed.g2.bx.psu.edu/repos/iuc/snp_sites/snp_sites/2.5.1+galaxy0 Finds SNP sites Keep only variable positions
toolshed.g2.bx.psu.edu/repos/iuc/snp_dists/snp_dists/0.6.3+galaxy0 SNP distance matrix Calculate SNP distances

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.9+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/snp_dists/snp_dists/0.6.3+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/snp_sites/snp_sites/2.5.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.1.3+galaxy0 View in ToolShed

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

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
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 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:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
2 679ca224e 2022-03-16 09:30:16 update tag
1 2e7ba7852 2022-03-16 09:24:13 tweak

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