diploid

variant-analysis-dip/diploid

Author(s)
Anton Nekrutenko, Nicola Soranzo
Version
4
Last updated
Apr 28, 2025
License
AGPL-3.0-or-later
Tags
variant-analysis

Features
Tutorial
Calling variants in diploid systems
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00257
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nGIAB-Ashkenazim-Trio-hg19.bam"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nGIAB-Ashkenazim-Trio.tabular"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["FreeBayes"];
  0 -->|output| 2;
  3["VcfAllelicPrimitives:"];
  2 -->|output_vcf| 3;
  4["SnpEff eff:"];
  3 -->|out_file1| 4;
  5["GEMINI load"];
  4 -->|snpeff_output| 5;
  1 -->|output| 5;
  6["GEMINI_query2"];
  5 -->|outfile| 6;
  7["GEMINI_db_info"];
  5 -->|outfile| 7;
  8["GEMINI_query1"];
  5 -->|outfile| 8;

Inputs

Input Label
Input dataset GIAB-Ashkenazim-Trio-hg19.bam
Input dataset GIAB-Ashkenazim-Trio.tabular

Outputs

From Output Label

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.9+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/gemini_db_info/gemini_db_info/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/gemini_query/gemini_query/0.20.1+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.2+galaxy0 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
  1. Click on Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
  2. Click on Import at the top-right of the screen
  3. 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”
  4. 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
5 b47672f8a 2025-04-28 08:14:48 change name
4 f1da07eda 2025-04-23 13:40:37 update tutorial and test workflow
3 667ff3de9 2020-01-22 10:59:29 annotation
2 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
1 a294ecfbb 2018-12-07 12:30:56 workflow for diploid

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/dip/workflows/diploid.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