Trio Analysis Tutorial

Run Workflow in Galaxy

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

flowchart TD
  0["EGA Download Client"];
  85672f3a-1556-49b6-be09-2e6c81721fb3["Output\nEGA Download Client: authorized datasets"];
  0 --> 85672f3a-1556-49b6-be09-2e6c81721fb3;
  style 85672f3a-1556-49b6-be09-2e6c81721fb3 stroke:#2c3143,stroke-width:4px;
  1["EGA Download Client"];
  acd2bcf0-4b9d-4743-9034-716e73d4824f["Output\nList of files in EGAD00001008392"];
  1 --> acd2bcf0-4b9d-4743-9034-716e73d4824f;
  style acd2bcf0-4b9d-4743-9034-716e73d4824f stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\npedigree"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Search in textfiles"];
  1 -->|dataset_file_list| 3;
  6d5d135e-a373-4938-9374-019a09f45a51["Output\nList of Case 5 VCFs"];
  3 --> 6d5d135e-a373-4938-9374-019a09f45a51;
  style 6d5d135e-a373-4938-9374-019a09f45a51 stroke:#2c3143,stroke-width:4px;
  4["EGA Download Client"];
  3 -->|output| 4;
  bdce7169-390b-4adb-9305-5550d5d70a73["Output\nCase 5 VCFs.gz"];
  4 --> bdce7169-390b-4adb-9305-5550d5d70a73;
  style bdce7169-390b-4adb-9305-5550d5d70a73 stroke:#2c3143,stroke-width:4px;
  5["Convert compressed file to uncompressed."];
  4 -->|downloaded_file_collection| 5;
  82b71cdc-d813-4c77-8ff3-fa59e1725709["Output\nCase 5 VCFs"];
  5 --> 82b71cdc-d813-4c77-8ff3-fa59e1725709;
  style 82b71cdc-d813-4c77-8ff3-fa59e1725709 stroke:#2c3143,stroke-width:4px;
  6["Column Regex Find And Replace"];
  5 -->|output1| 6;
  5e1ff158-cf8a-4dc8-9c22-b987a9f5ac27["Output\nCase 5 VCFs (Fixed Header and Chr)"];
  6 --> 5e1ff158-cf8a-4dc8-9c22-b987a9f5ac27;
  style 5e1ff158-cf8a-4dc8-9c22-b987a9f5ac27 stroke:#2c3143,stroke-width:4px;
  7["bcftools norm"];
  6 -->|out_file1| 7;
  96b34c8d-fa92-48cb-b01f-c05364deba5d["Output\nCase 5 Normalized VCFs"];
  7 --> 96b34c8d-fa92-48cb-b01f-c05364deba5d;
  style 96b34c8d-fa92-48cb-b01f-c05364deba5d stroke:#2c3143,stroke-width:4px;
  8["Filter"];
  7 -->|output_file| 8;
  a8539eb9-8bc3-473b-a27f-201c3acf5539["Output\nCase 5 Normalized VCFs (Removed )"];
  8 --> a8539eb9-8bc3-473b-a27f-201c3acf5539;
  style a8539eb9-8bc3-473b-a27f-201c3acf5539 stroke:#2c3143,stroke-width:4px;
  9["bcftools merge"];
  8 -->|out_file1| 9;
  b5c479b2-e58a-4fe2-b1cf-fc64476c8192["Output\nCase 5 Merged VCF"];
  9 --> b5c479b2-e58a-4fe2-b1cf-fc64476c8192;
  style b5c479b2-e58a-4fe2-b1cf-fc64476c8192 stroke:#2c3143,stroke-width:4px;
  10["SnpEff eff:"];
  9 -->|output_file| 10;
  cd7b4941-4f4c-4631-8ad5-3411e60fbbd9["Output\nCase 5 SnpEff Annotated vcf"];
  10 --> cd7b4941-4f4c-4631-8ad5-3411e60fbbd9;
  style cd7b4941-4f4c-4631-8ad5-3411e60fbbd9 stroke:#2c3143,stroke-width:4px;
  11["Convert uncompressed file to compressed"];
  10 -->|snpeff_output| 11;
  6e5e1084-b5e1-4daf-8f3b-bd3868a52a25["Output\nSnpEff Annotated vcf_bgzip"];
  11 --> 6e5e1084-b5e1-4daf-8f3b-bd3868a52a25;
  style 6e5e1084-b5e1-4daf-8f3b-bd3868a52a25 stroke:#2c3143,stroke-width:4px;
  12["gene.iobio visualisation"];
  11 -->|output1| 12;
  11 -->|output1| 12;
  11 -->|output1| 12;
  0b30f4e0-7328-4479-8a56-bbf828fcfdba["Output\nCase 5 gene.iobio results"];
  12 --> 0b30f4e0-7328-4479-8a56-bbf828fcfdba;
  style 0b30f4e0-7328-4479-8a56-bbf828fcfdba stroke:#2c3143,stroke-width:4px;
  13["Case 5 GEMINI Database"];
  11 -->|output1| 13;
  2 -->|output| 13;
  8a1964d9-607c-4dd3-a2dc-0f9a68dbb681["Output\nGEMINI Database"];
  13 --> 8a1964d9-607c-4dd3-a2dc-0f9a68dbb681;
  style 8a1964d9-607c-4dd3-a2dc-0f9a68dbb681 stroke:#2c3143,stroke-width:4px;
  14["Case 5 GEMINI Inheritance pattern"];
  13 -->|outfile| 14;
  960ef978-089c-4292-81b5-731965c72a0d["Output\nCase 5 GEMINI results"];
  14 --> 960ef978-089c-4292-81b5-731965c72a0d;
  style 960ef978-089c-4292-81b5-731965c72a0d stroke:#2c3143,stroke-width:4px;

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/trio-analysis/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