Workflows

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.

pox-virus-tiled-amplicon-ref-masking
Viktoria Isabel Schwarz, Wolfgang Maier

Last updated May 22, 2023

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

Download Galaxy Workflow.ga Galaxy Australia Galaxy Main Galaxy France Galaxy Europe Import to another server (≥23.0+ only!) 
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;
  5["Datamash"];
  2 -->|out_file1| 5;
  6["Datamash"];
  3 -->|out_file1| 6;
  7["Cut"];
  4 -->|output| 7;
  8["Compute"];
  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;
  af755a5e-2b20-49bc-9d52-34781f937f48["Output\nmasked_ref_pool2"];
  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;
  0c3b5b20-c426-428c-a08b-c835a82477c1["Output\nmasked_ref_pool1"];
  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 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