Microbial Variant Calling

variant-analysis-microbial-variants/microbial-variant-calling

Author(s)

Version
4
Last updated
Jan 23, 2020
License
None Specified, defaults to CC-BY-4.0
Tags
variant-analysis

Features
Tutorial
Microbial Variant Calling
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00263
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nInput dataset"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nInput dataset"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nInput dataset"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nInput dataset"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nInput dataset"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["snippy"];
  0 -->|output| 5;
  1 -->|output| 5;
  3 -->|output| 5;
  e7857f88-6ace-46c6-9b1f-f9fd1afdebfd["Output\nsnippy_fasta"];
  5 --> e7857f88-6ace-46c6-9b1f-f9fd1afdebfd;
  style e7857f88-6ace-46c6-9b1f-f9fd1afdebfd stroke:#2c3143,stroke-width:4px;
  52884e5d-57c3-4954-81f0-72538bba1189["Output\nsnippy_tabular"];
  5 --> 52884e5d-57c3-4954-81f0-72538bba1189;
  style 52884e5d-57c3-4954-81f0-72538bba1189 stroke:#2c3143,stroke-width:4px;
  6["JBrowse"];
  5 -->|snpgff| 6;
  4 -->|output| 6;
  5 -->|snpsbam| 6;
  2 -->|output| 6;
  11e76472-72bf-40d9-9f3a-ceb576c6d2c9["Output\njbrowse_html"];
  6 --> 11e76472-72bf-40d9-9f3a-ceb576c6d2c9;
  style 11e76472-72bf-40d9-9f3a-ceb576c6d2c9 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset
Input dataset
Input dataset
Input dataset
Input dataset

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2 snippy
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/0.7.0.3 JBrowse

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/0.7.0.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2 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 667ff3de9 2020-01-22 10:59:29 annotation
4 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
3 dfb973603 2018-05-12 07:20:37 annotate workflow outputs
2 8803cca01 2018-05-12 07:17:32 pretty'fy workflow
1 5a1bff422 2018-04-06 19:46:09 Add some love to microbial variant calling tutorial (#732)

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/microbial-variants/workflows/microbial_variant_calling.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