Workflow 1: Preprocessing

Run Workflow in Galaxy

• Galaxy Australia
• Galaxy Main
• Galaxy France
• Galaxy Europe
• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Dataset\nT1A_forward"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nT1A_reverse"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Quality control Forward"];
  0 -->|output| 2;
  025f2766-0802-461e-afbd-a716e6f81ba8["Output\nFastQC on input dataset(s): RawData"];
  2 --> 025f2766-0802-461e-afbd-a716e6f81ba8;
  style 025f2766-0802-461e-afbd-a716e6f81ba8 stroke:#2c3143,stroke-width:4px;
  a54ee2fd-7bce-439a-9f1f-f9ec9bf00efd["Output\nFastQC on input dataset(s): Webpage"];
  2 --> a54ee2fd-7bce-439a-9f1f-f9ec9bf00efd;
  style a54ee2fd-7bce-439a-9f1f-f9ec9bf00efd stroke:#2c3143,stroke-width:4px;
  3["Quality control Reverse"];
  1 -->|output| 3;
  4["Cutadapt"];
  0 -->|output| 4;
  1 -->|output| 4;
  4bc7c8a4-b985-41dd-b67f-a3dfecd38a67["Output\nCutadapt on input dataset(s): Read 1 Output"];
  4 --> 4bc7c8a4-b985-41dd-b67f-a3dfecd38a67;
  style 4bc7c8a4-b985-41dd-b67f-a3dfecd38a67 stroke:#2c3143,stroke-width:4px;
  36ec0bba-e49a-47e2-b916-afec9b35cc3e["Output\nCutadapt on input dataset(s): Read 2 Output"];
  4 --> 36ec0bba-e49a-47e2-b916-afec9b35cc3e;
  style 36ec0bba-e49a-47e2-b916-afec9b35cc3e stroke:#2c3143,stroke-width:4px;
  5["MultiQC"];
  2 -->|text_file| 5;
  3 -->|text_file| 5;
  b9ca2123-0ee0-40a0-b2ec-cfc94fa35849["Output\nMultiQC on input dataset(s): Stats"];
  5 --> b9ca2123-0ee0-40a0-b2ec-cfc94fa35849;
  style b9ca2123-0ee0-40a0-b2ec-cfc94fa35849 stroke:#2c3143,stroke-width:4px;
  e94ceb7a-0d6b-41c8-b79d-035b315e0a06["Output\nMultiQC on input dataset(s): Webpage"];
  5 --> e94ceb7a-0d6b-41c8-b79d-035b315e0a06;
  style e94ceb7a-0d6b-41c8-b79d-035b315e0a06 stroke:#2c3143,stroke-width:4px;
  6["rRNA/rDNA selection"];
  4 -->|out1| 6;
  4 -->|out2| 6;
  7["FASTQ interlacer"];
  6 -->|unaligned_forward| 7;
  6 -->|unaligned_reverse| 7;
  b060eebc-cd14-486e-806e-aae983bdf52d["Output\nFASTQ interlacer singles from input dataset(s)"];
  7 --> b060eebc-cd14-486e-806e-aae983bdf52d;
  style b060eebc-cd14-486e-806e-aae983bdf52d stroke:#2c3143,stroke-width:4px;
  70b738db-5451-4eaa-91c0-eb445be297fb["Output\nFASTQ interlacer pairs from input dataset(s)"];
  7 --> 70b738db-5451-4eaa-91c0-eb445be297fb;
  style 70b738db-5451-4eaa-91c0-eb445be297fb stroke:#2c3143,stroke-width:4px;

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/microbiome/tutorials/metatranscriptomics-short/workflows/workflow1_preprocessing.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