Calling variants in non-diploid systems

variant-analysis-non-dip/calling-variants-in-non-diploid-systems

Author(s)

Version
5
Last updated
Oct 23, 2020
License
None Specified, defaults to CC-BY-4.0
Tags
variant-analysis

Features
Tutorial
Calling variants in non-diploid systems
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00264
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\nraw_child-ds-1.fq"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nraw_child-ds-2.fq"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nraw_mother-ds-1.fq"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nraw_mother-ds-2.fq"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["FastQC"];
  0 -->|output| 4;
  5["FastQC"];
  1 -->|output| 5;
  6["Map with BWA-MEM"];
  0 -->|output| 6;
  1 -->|output| 6;
  7["FastQC"];
  2 -->|output| 7;
  8["FastQC"];
  3 -->|output| 8;
  9["Map with BWA-MEM"];
  2 -->|output| 9;
  3 -->|output| 9;
  10["MergeSamFiles"];
  9 -->|bam_output| 10;
  6 -->|bam_output| 10;
  11["MarkDuplicates"];
  10 -->|outFile| 11;
  12["BamLeftAlign"];
  11 -->|outFile| 12;
  13["Filter"];
  12 -->|output_bam| 13;
  14["FreeBayes"];
  13 -->|out_file1| 14;
  15["VCFfilter:"];
  14 -->|output_vcf| 15;
  16["VCFtoTab-delimited:"];
  15 -->|out_file1| 16;
  17["Cut"];
  16 -->|out_file1| 17;
  f2e84a79-a71f-4b5f-a526-55d8cd472a05["Output\ncut_variants"];
  17 --> f2e84a79-a71f-4b5f-a526-55d8cd472a05;
  style f2e84a79-a71f-4b5f-a526-55d8cd472a05 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

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 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
5 5b87c7df6 2020-10-23 22:37:45 Fix workflow.
4 d3d9d2eef 2020-10-23 21:56:59 Fix workflow parameters.
3 20545ace5 2020-10-23 21:43:48 Add workflow test.
2 6cd2c31a7 2020-10-23 21:23:05 Update workflow.
1 3b2d76cce 2020-02-07 17:31:13 workflow made for variant analysis tutorial

For Admins

Installing the workflow tools

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