Workflows

These workflows are associated with M. tuberculosis Variant Analysis

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.

M. tuberculosis Variant Analysis tutorial
Peter van Heusden

Last updated Sep 25, 2023

Launch in Tutorial Mode
License: MIT
Tests: ✅ Results: Not yet automated

Download Galaxy Workflow.ga Galaxy France Galaxy Australia Galaxy Europe Galaxy Main Import to another server (≥23.0+ only!) 
flowchart TD
  0["ℹ️ Input Dataset\nRead 1"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nRead 2"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nGenbank reference genome"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nGenome annotation GFF3"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nFASTA reference genome"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["FastQC"];
  0 -->|output| 5;
  6["FastQC"];
  1 -->|output| 6;
  7["Trimmomatic"];
  0 -->|output| 7;
  1 -->|output| 7;
  8["MultiQC"];
  6 -->|text_file| 8;
  5 -->|text_file| 8;
  8b6d9b61-619b-4509-b8ff-b89a3c37c528["Output\nmtbva_multiqc_webpage"];
  8 --> 8b6d9b61-619b-4509-b8ff-b89a3c37c528;
  style 8b6d9b61-619b-4509-b8ff-b89a3c37c528 stroke:#2c3143,stroke-width:4px;
  9["snippy"];
  7 -->|fastq_out_r1_paired| 9;
  7 -->|fastq_out_r2_paired| 9;
  2 -->|output| 9;
  f08867c3-1ef9-4b60-b3bc-50c54355729e["Output\nmtbva_snippy_vcf"];
  9 --> f08867c3-1ef9-4b60-b3bc-50c54355729e;
  style f08867c3-1ef9-4b60-b3bc-50c54355729e stroke:#2c3143,stroke-width:4px;
  fbd56a0e-978f-4dad-ad65-7e6a04df871a["Output\nmtbva_snippy_variants_table"];
  9 --> fbd56a0e-978f-4dad-ad65-7e6a04df871a;
  style fbd56a0e-978f-4dad-ad65-7e6a04df871a stroke:#2c3143,stroke-width:4px;
  10["Kraken2"];
  7 -->|fastq_out_r1_paired| 10;
  7 -->|fastq_out_r2_paired| 10;
  bbb7a59f-a352-4780-a77f-5e1127ae1f31["Output\nmtbva_kraken_report"];
  10 --> bbb7a59f-a352-4780-a77f-5e1127ae1f31;
  style bbb7a59f-a352-4780-a77f-5e1127ae1f31 stroke:#2c3143,stroke-width:4px;
  11["TB Variant Filter"];
  9 -->|snpvcf| 11;
  12["TB-Profiler Profile"];
  9 -->|snpsbam| 12;
  13["JBrowse"];
  4 -->|output| 13;
  9 -->|snpsbam| 13;
  11 -->|output1| 13;
  3 -->|output| 13;
  cebc6e6d-5fc8-4e28-9a0b-f2f5717f0ec1["Output\nmtbva_jbrowse"];
  13 --> cebc6e6d-5fc8-4e28-9a0b-f2f5717f0ec1;
  style cebc6e6d-5fc8-4e28-9a0b-f2f5717f0ec1 stroke:#2c3143,stroke-width:4px;
  14["TB Variant Report"];
  9 -->|snpvcf| 14;
  12 -->|results_json| 14;
  5b51f4fb-4f8f-4b20-a411-a4d9ac60652b["Output\nmtbva_tb_variant_dr_report_html"];
  14 --> 5b51f4fb-4f8f-4b20-a411-a4d9ac60652b;
  style 5b51f4fb-4f8f-4b20-a411-a4d9ac60652b stroke:#2c3143,stroke-width:4px;
  98e3dd70-7d44-41b1-ae57-c21aa975dad5["Output\nmtbva_tb_variant_report_html"];
  14 --> 98e3dd70-7d44-41b1-ae57-c21aa975dad5;
  style 98e3dd70-7d44-41b1-ae57-c21aa975dad5 stroke:#2c3143,stroke-width:4px;

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: