TB variants tutorial main workflow

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nMycobacterium_tuberculosis_ancestral_reference.gbk"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nMycobacterium_tuberculosis_h37rv.ASM19595v2.45.chromosome.Chromosome.gff3"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Collection\nInput Dataset Collection"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["seqret"];
  0 -->|output| 3;
  4["fastp"];
  2 -->|output| 4;
  5["Flatten collection"];
  2 -->|output| 5;
  6["snippy"];
  4 -->|output_paired_coll| 6;
  0 -->|output| 6;
  7["Kraken2"];
  4 -->|output_paired_coll| 7;
  8["FastQC"];
  5 -->|output| 8;
  9["TB Variant Filter"];
  6 -->|snpvcf| 9;
  10["TB-Profiler Profile"];
  6 -->|snpsbam| 10;
  11["MultiQC"];
  8 -->|text_file| 11;
  12["JBrowse"];
  3 -->|out_file1| 12;
  6 -->|snpsbam| 12;
  9 -->|output1| 12;
  1 -->|output| 12;
  13["Text transformation"];
  9 -->|output1| 13;
  14["TB Variant Report"];
  13 -->|output| 14;
  10 -->|results_json| 14;

Inputs

Outputs

Tools

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

1. Click on galaxy-workflows-activity Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
2. Click on galaxy-upload Import at the top-right of the screen
3. 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”
4. 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/variant-analysis/tutorials/tb-variant-analysis/workflows/TB-variants-tutorial-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