Metatranscriptomics analysis using microbiome RNA-seq data - Workflow 1: Preprocessing

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nReverse raw reads"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nForward raw reads"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["FastQC"];
  0 -->|output| 2;
  676cd11f-0479-47c4-a23b-c6c8ed5a7790["Output\nfastqc_reverse_html_file"];
  2 --> 676cd11f-0479-47c4-a23b-c6c8ed5a7790;
  style 676cd11f-0479-47c4-a23b-c6c8ed5a7790 stroke:#2c3143,stroke-width:4px;
  3["FastQC"];
  1 -->|output| 3;
  1fb52b78-c905-43c7-a295-d628c996d35a["Output\nfastqc_forward_html_file"];
  3 --> 1fb52b78-c905-43c7-a295-d628c996d35a;
  style 1fb52b78-c905-43c7-a295-d628c996d35a stroke:#2c3143,stroke-width:4px;
  4["Cutadapt"];
  1 -->|output| 4;
  0 -->|output| 4;
  0e7406ed-9eca-486e-b19a-4cbbf04b5138["Output\ncutadapt_report"];
  4 --> 0e7406ed-9eca-486e-b19a-4cbbf04b5138;
  style 0e7406ed-9eca-486e-b19a-4cbbf04b5138 stroke:#2c3143,stroke-width:4px;
  5["MultiQC"];
  3 -->|text_file| 5;
  2 -->|text_file| 5;
  d9f371dd-aa6c-4540-b62b-0e34c0b71afa["Output\nmultiqc_html_report"];
  5 --> d9f371dd-aa6c-4540-b62b-0e34c0b71afa;
  style d9f371dd-aa6c-4540-b62b-0e34c0b71afa stroke:#2c3143,stroke-width:4px;
  6["Filter with SortMeRNA"];
  4 -->|out1| 6;
  4 -->|out2| 6;
  3092eb62-d7fc-4d66-bf57-4c6cf491d0e3["Output\nsortmerna_unaligned_reverse"];
  6 --> 3092eb62-d7fc-4d66-bf57-4c6cf491d0e3;
  style 3092eb62-d7fc-4d66-bf57-4c6cf491d0e3 stroke:#2c3143,stroke-width:4px;
  db3bb8ee-8af7-4528-be4b-f3ea6d381856["Output\nsortmerna_unaligned_forward"];
  6 --> db3bb8ee-8af7-4528-be4b-f3ea6d381856;
  style db3bb8ee-8af7-4528-be4b-f3ea6d381856 stroke:#2c3143,stroke-width:4px;
  7["FASTQ interlacer"];
  6 -->|unaligned_forward| 7;
  6 -->|unaligned_reverse| 7;

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

1. Click on galaxy-workflows-activity Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
2. Click on galaxy-upload Import at the top-right of the screen
3. 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”
4. 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