Workflow constructed from history 'Tuto Obitools'

Run Workflow in Galaxy

• Galaxy Australia
• Galaxy France
• Galaxy Main
• 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;

Inputs

Outputs

Tools

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.

Importing into Galaxy

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:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/ecology/tutorials/Obitools-metabarcoding/workflows/main_workflow.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows