These workflows are associated with Trio Analysis using Synthetic Datasets from RD-Connect GPAP

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.

Trio Analysis Tutorial
Jasper Ouwerkerk

Last updated Jul 11, 2023

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

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;
  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;

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 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: