Workflow 1: Preprocessing

microbiome-metatranscriptomics-short/workflow1-preprocessing

Author(s)
Bérénice Batut, Pratik Jagtap, Subina Mehta, Ray Sajulga, Emma Leith, Praveen Kumar, Saskia Hiltemann, Paul Zierep
Version
1
Last updated
Jan 15, 2024
License
MIT
Tags

Features
Tutorial
Metatranscriptomics analysis using microbiome RNA-seq data (short)
Other workflows associated with this material
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00128
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
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;

Inputs

Input Label
Input dataset T1A_forward
Input dataset T1A_reverse

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 FastQC Quality control Forward
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 FastQC Quality control Reverse
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1 Cutadapt
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1 MultiQC
toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/2.1b.6 Filter with SortMeRNA rRNA/rDNA selection
toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0 FASTQ interlacer

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/2.1b.6 View in ToolShed

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

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

Version History

Version Commit Time Comments
1 0e0a2f2cc 2024-01-10 15:47:09 Rename metagenomics topic to microbiome

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