Workflow 1: Preprocessing
microbiome-metatranscriptomics-short/workflow1-preprocessing
Launch in Tutorial Mode
question
galaxy-download Download
galaxy-download 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
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 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:
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