TB Variant Analysis v1.0

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Collection\nReads"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nReference Genome"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Parameter\nMinimum depth of coverage"];
  style 2 fill:#ded,stroke:#393,stroke-width:4px;
  3["ℹ️ Input Parameter\nMinimum variant allele frequency"];
  style 3 fill:#ded,stroke:#393,stroke-width:4px;
  4["ℹ️ Input Parameter\nAdditional BWA-MEM options"];
  style 4 fill:#ded,stroke:#393,stroke-width:4px;
  5["fastp"];
  0 -->|output| 5;
  6["seqret"];
  1 -->|output| 6;
  7["snippy"];
  4 -->|output| 7;
  2 -->|output| 7;
  3 -->|output| 7;
  5 -->|output_paired_coll| 7;
  1 -->|output| 7;
  8["Kraken2"];
  5 -->|output_paired_coll| 8;
  c7abf2bf-ed4c-433e-a695-9eca61282bb5["Output\nreport_output"];
  8 --> c7abf2bf-ed4c-433e-a695-9eca61282bb5;
  style c7abf2bf-ed4c-433e-a695-9eca61282bb5 stroke:#2c3143,stroke-width:4px;
  083a0e51-7780-4c91-a071-dc0e4641d060["Output\noutput"];
  8 --> 083a0e51-7780-4c91-a071-dc0e4641d060;
  style 083a0e51-7780-4c91-a071-dc0e4641d060 stroke:#2c3143,stroke-width:4px;
  9["QualiMap BamQC"];
  7 -->|snpsbam| 9;
  10["mosdepth"];
  2 -->|output| 10;
  7 -->|snpsbam| 10;
  11["TB Variant Filter"];
  7 -->|snpvcf| 11;
  12["TB-Profiler Profile"];
  7 -->|snpsbam| 12;
  335635b4-a4de-4980-ad02-68f0035daeaa["Output\noutput_txt"];
  12 --> 335635b4-a4de-4980-ad02-68f0035daeaa;
  style 335635b4-a4de-4980-ad02-68f0035daeaa stroke:#2c3143,stroke-width:4px;
  13["TB Variant Filter"];
  7 -->|snpvcf| 13;
  14["Flatten collection"];
  9 -->|raw_data| 14;
  15["Text reformatting"];
  10 -->|output_quantized_bed| 15;
  16["Text transformation"];
  11 -->|output1| 16;
  007df8c2-bd13-495f-8904-abf31d4594d0["Output\nFinal annotated VCF"];
  16 --> 007df8c2-bd13-495f-8904-abf31d4594d0;
  style 007df8c2-bd13-495f-8904-abf31d4594d0 stroke:#2c3143,stroke-width:4px;
  17["MultiQC"];
  5 -->|report_json| 17;
  14 -->|output| 17;
  59528235-7525-4ef9-8810-36f1ed0f01f6["Output\nhtml_report"];
  17 --> 59528235-7525-4ef9-8810-36f1ed0f01f6;
  style 59528235-7525-4ef9-8810-36f1ed0f01f6 stroke:#2c3143,stroke-width:4px;
  18["bcftools consensus"];
  13 -->|output1| 18;
  6 -->|out_file1| 18;
  15 -->|outfile| 18;
  c71b135d-35f9-44d0-a20e-f25528e518af["Output\nconsensus_genome"];
  18 --> c71b135d-35f9-44d0-a20e-f25528e518af;
  style c71b135d-35f9-44d0-a20e-f25528e518af stroke:#2c3143,stroke-width:4px;
  19["TB Variant Report"];
  16 -->|output| 19;
  12 -->|results_json| 19;
  959528d2-f8f2-4440-99cf-44fddd6c5069["Output\ndrug_resistance_report_html"];
  19 --> 959528d2-f8f2-4440-99cf-44fddd6c5069;
  style 959528d2-f8f2-4440-99cf-44fddd6c5069 stroke:#2c3143,stroke-width:4px;
  4d9636eb-075b-4fd2-a1e4-1a7c37a17fc0["Output\nvariants_report_html"];
  19 --> 4d9636eb-075b-4fd2-a1e4-1a7c37a17fc0;
  style 4d9636eb-075b-4fd2-a1e4-1a7c37a17fc0 stroke:#2c3143,stroke-width:4px;

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

• 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/variant-analysis/tutorials/tb-variant-analysis/workflows/tb-variant-analysis.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