Workflows

These workflows are associated with Calling variants in non-diploid systems

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.

Calling variants in non-diploid systems

Last updated Oct 24, 2020

Launch in Tutorial Mode
License: None Specified, defaults to CC-BY-4.0
Tests: ✅ Results: Not yet automated

Download Galaxy Workflow.ga Galaxy Europe Galaxy Australia Galaxy France Galaxy Main Import to another server (≥23.0+ only!) 
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;

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