Workflows

These workflows are associated with RAD-Seq Reference-based data analysis

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.

Workflow Constructed From History 'STACKS RAD: Population Genomics With Reference Genome'

Last updated Jan 22, 2020

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

Download Galaxy Workflow.ga EU US AU Import to another server (≥23.0+ only!) 
flowchart TD
  0["Input dataset"];
  1["Input dataset"];
  10["FastQC"];
  11["Map with BWA"];
  12["Select"];
  13["Select"];
  14["Replace Text"];
  15["Replace Text"];
  16["Replace Text"];
  17["MultiQC"];
  18["Replace Text"];
  19["Replace Text"];
  2["Input dataset"];
  20["Add column"];
  21["Concatenate datasets"];
  22["Cut"];
  23["Convert"];
  24["Regex Replace"];
  25["Stacks: reference map"];
  26["Stacks: populations"];
  27["Summary Statistics"];
  28["Sort"];
  29["Count"];
  3["Input dataset"];
  30["Filter"];
  4["Stacks: process radtags"];
  5["Stacks: process radtags"];
  6["Stacks: process radtags"];
  7["Replace Text"];
  8["Select"];
  9["Select"];
  5 -->|demultiplexed| 10;
  5 -->|demultiplexed| 11;
  3 -->|output| 11;
  6 -->|output_log| 12;
  6 -->|output_log| 13;
  7 -->|outfile| 14;
  8 -->|out_file1| 15;
  9 -->|out_file1| 16;
  10 -->|text_file| 17;
  12 -->|out_file1| 18;
  13 -->|out_file1| 19;
  14 -->|outfile| 20;
  19 -->|outfile| 21;
  15 -->|outfile| 21;
  16 -->|outfile| 21;
  18 -->|outfile| 21;
  20 -->|out_file1| 22;
  21 -->|out_file1| 23;
  22 -->|out_file1| 24;
  11 -->|bam_output| 25;
  24 -->|outfile| 25;
  25 -->|all_output| 26;
  24 -->|outfile| 26;
  26 -->|out_fstats| 27;
  26 -->|out_fstats| 28;
  26 -->|out_fstats| 29;
  26 -->|out_fstats| 30;
  1 -->|output| 4;
  0 -->|output| 4;
  1 -->|output| 5;
  0 -->|output| 5;
  1 -->|output| 6;
  0 -->|output| 6;
  2 -->|output| 7;
  4 -->|output_log| 8;
  5 -->|output_log| 9;
Ref Based Rad Seq

Last updated Jan 22, 2020

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

Download Galaxy Workflow.ga EU US AU Import to another server (≥23.0+ only!) 
flowchart TD
  0["Input dataset"];
  1["Input dataset"];
  2["Input dataset"];
  3["Input dataset"];
  4["Stacks: process radtags"];
  5["Stacks: process radtags"];
  6["Stacks: process radtags"];
  7["Map with BWA for Illumina"];
  8["Stacks: reference map"];
  9["Stacks: populations"];
  2 -->|output| 4;
  3 -->|output| 4;
  2 -->|output| 5;
  3 -->|output| 5;
  2 -->|output| 6;
  3 -->|output| 6;
  0 -->|output| 7;
  4 -->|demultiplexed| 7;
  7 -->|output| 8;
  1 -->|output| 8;
  8 -->|all_output| 9;
  1 -->|output| 9;

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: