These workflows are associated with Pox virus genome analysis from tiled-amplicon sequencing data

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.

Viktoria Isabel Schwarz, Wolfgang Maier

Last updated May 22, 2023

Launch in Tutorial Mode question
License: MIT
Tests: ✅ Results: Not yet automated

flowchart TD
  0["ℹ️ Input Dataset\nPrimer Scheme"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nReference FASTA"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Select pool1 primers"];
  0 -->|output| 2;
  3["Select pool2 primers"];
  0 -->|output| 3;
  4["Compute sequence length"];
  1 -->|output| 4;
  2 -->|out_file1| 5;
  3 -->|out_file1| 6;
  4 -->|output| 7;
  5 -->|out_file| 8;
  9["Get start position of Pool2"];
  6 -->|out_file| 9;
  10["Get end position of sequence"];
  7 -->|out_file1| 10;
  11["Get end position of Pool1"];
  8 -->|out_file1| 11;
  12["Compose text parameter value"];
  9 -->|text_param| 12;
  13["Compose text parameter value"];
  11 -->|text_param| 13;
  10 -->|text_param| 13;
  14["Mask Reference for Pool2"];
  1 -->|output| 14;
  12 -->|out1| 14;
  14 --> af755a5e-2b20-49bc-9d52-34781f937f48;
  style af755a5e-2b20-49bc-9d52-34781f937f48 stroke:#2c3143,stroke-width:4px;
  15["Mask Reference for Pool1"];
  1 -->|output| 15;
  13 -->|out1| 15;
  15 --> 0c3b5b20-c426-428c-a08b-c835a82477c1;
  style 0c3b5b20-c426-428c-a08b-c835a82477c1 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 galaxy-upload 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