Workflows

These workflows are associated with Metabarcoding/eDNA through Obitools

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 'Tuto Obitools'

Last updated Feb 28, 2022

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

Download Galaxy Workflow.ga Galaxy Main Galaxy Australia Galaxy France Galaxy Europe Import to another server (≥23.0+ only!) 
flowchart TD
  0["ℹ️ Input Dataset\nwolf_tutorial.zip?download=1"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Illuminapairedend"];
  2["Unzip"];
  0 -->|output| 2;
  3["FastQC"];
  1 -->|output| 3;
  4["FASTQ Groomer"];
  1 -->|output| 4;
  5["obigrep"];
  4 -->|output_file| 5;
  6["Line/Word/Character count"];
  4 -->|output_file| 6;
  7["Line/Word/Character count"];
  5 -->|output| 7;
  8["NGSfilter"];
  5 -->|output| 8;
  9["obiuniq"];
  8 -->|output| 9;
  10["obiannotate"];
  9 -->|output| 10;
  11["obistat"];
  10 -->|output| 11;
  12["obigrep"];
  10 -->|output| 12;
  13["obigrep"];
  12 -->|output| 13;
  14["obiclean"];
  13 -->|output| 14;
  15["NCBI BLAST+ blastn"];
  14 -->|output| 15;
  16["Filter sequences by ID"];
  15 -->|output1| 16;
  17["Filter sequences by ID"];
  15 -->|output1| 17;
  14 -->|output| 17;
  18["obitab"];
  16 -->|output_pos| 18;
  19["obitab"];
  17 -->|output_pos| 19;
  20["Join two Datasets"];
  19 -->|output| 20;
  15 -->|output1| 20;
  21["Join two Datasets"];
  20 -->|out_file1| 21;
  18 -->|output| 21;
  22["Cut"];
  21 -->|out_file1| 22;
  23["Filter"];
  22 -->|out_file1| 23;

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