Trio Analysis Tutorial

variant-analysis-trio-analysis/main-workflow

Author(s)
Jasper Ouwerkerk
version Version
5
last_modification Last updated
Jul 11, 2023
license License
MIT
galaxy-tags Tags
variant-analysis

Features

Tutorial
hands_on Trio Analysis using Synthetic Datasets from RD-Connect GPAP

Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00270
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode question
galaxy-download Download
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;

Inputs

Input Label
Input dataset pedigree

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/ega_download_client/pyega3/5.0.2+galaxy0 EGA Download Client
toolshed.g2.bx.psu.edu/repos/iuc/ega_download_client/pyega3/5.0.2+galaxy0 EGA Download Client
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1 Search in textfiles
toolshed.g2.bx.psu.edu/repos/iuc/ega_download_client/pyega3/5.0.2+galaxy0 EGA Download Client
CONVERTER_gz_to_uncompressed Convert compressed file to uncompressed.
toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1 Column Regex Find And Replace
toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.9+galaxy1 bcftools norm
Filter1 Filter
toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10 bcftools merge
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1 SnpEff eff:
CONVERTER_uncompressed_to_gz Convert uncompressed file to compressed
toolshed.g2.bx.psu.edu/repos/iuc/geneiobio/gene_iobio_display_generation_iframe/4.7.1 gene.iobio visualisation
toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2 GEMINI load Case 5 GEMINI Database
toolshed.g2.bx.psu.edu/repos/iuc/gemini_inheritance/gemini_inheritance/0.20.1 GEMINI inheritance pattern Case 5 GEMINI Inheritance pattern

Tools

Tool Links
CONVERTER_gz_to_uncompressed
CONVERTER_uncompressed_to_gz
Filter1
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/bcftools_merge/bcftools_merge/1.10 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.9+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/ega_download_client/pyega3/5.0.2+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/gemini_inheritance/gemini_inheritance/0.20.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/geneiobio/gene_iobio_display_generation_iframe/4.7.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1 View in ToolShed

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

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:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
22 9623387f0 2023-07-11 13:31:04 Add gene.iobio
21 c7df03484 2023-07-10 14:25:39 Add gene.iobio to workflow
20 a133ddbaf 2023-05-16 13:21:21 Add EGA download client authorized dataset
19 89798a151 2023-05-16 13:18:41 Update PyEGA version in main_workflow.ga
18 890e3ed49 2023-03-24 10:58:24 add orcid
17 d20983843 2023-03-24 10:51:39 fix reator and workflow_output labels
16 588e52155 2023-03-21 16:13:33 now really add license
15 cdfd52652 2023-03-21 16:08:22 properly add license
14 49bda25d3 2023-03-21 15:57:57 rename workflow
13 79e4f95ac 2023-03-21 15:56:54 add test
12 9ba85fb0a 2023-03-21 15:45:54 update PyEGA version & add creator/license
11 b79cc70ea 2023-03-01 15:31:31 Update workflow with nice labels
10 4ed74364a 2022-05-10 12:43:15 Update workflow ( skip header)
9 2726695af 2022-05-03 13:57:30 add annotation and tag to workflow
8 0816782f5 2022-05-03 09:00:47 Update prefix pattern
7 4cb441ff6 2022-05-03 07:58:29 Move decompress step
6 e61e67133 2022-05-02 13:21:17 Replace AWK with Filter tool to remove sites
5 72a287e5e 2022-04-29 12:33:18 update tutorial
4 0e98aba15 2022-04-26 14:06:34 change workflow
3 1eca39b54 2022-04-20 13:52:04 Spelling check + testing workflow
2 129023b5f 2022-04-19 15:19:56 initial tutorial
1 4b2ff311b 2022-04-07 14:23:57 initial commit

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