MGnify's amplicon pipeline v5.0 - Quality control SE

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Collection\nSingle-end reads"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Parameter\nTrimmomatic - SLIDING WINDOW - Average quality required"];
  style 1 fill:#ded,stroke:#393,stroke-width:4px;
  2["ℹ️ Input Parameter\nTrimmomatic - LEADING"];
  style 2 fill:#ded,stroke:#393,stroke-width:4px;
  3["ℹ️ Input Parameter\nTrimmomatic - SLIDING WINDOW - Number of bases to average across"];
  style 3 fill:#ded,stroke:#393,stroke-width:4px;
  4["ℹ️ Input Parameter\nTrimmomatic - TRAILING"];
  style 4 fill:#ded,stroke:#393,stroke-width:4px;
  5["ℹ️ Input Parameter\nTrimmomatic - MINLEN"];
  style 5 fill:#ded,stroke:#393,stroke-width:4px;
  6["ℹ️ Input Parameter\nLength filtering - Minimum size"];
  style 6 fill:#ded,stroke:#393,stroke-width:4px;
  7["ℹ️ Input Parameter\nAmbiguity filtering - Maximal N percentage threshold to conserve sequences"];
  style 7 fill:#ded,stroke:#393,stroke-width:4px;
  8["FastQC"];
  0 -->|output| 8;
  9["Trimming"];
  1 -->|output| 9;
  3 -->|output| 9;
  2 -->|output| 9;
  4 -->|output| 9;
  5 -->|output| 9;
  0 -->|output| 9;
  10["Replace"];
  8 -->|text_file| 10;
  11["Length filtering"];
  9 -->|fastq_out| 11;
  6 -->|output| 11;
  12["FastQC"];
  9 -->|fastq_out| 12;
  13["Ambiguity filtering"];
  7 -->|output| 13;
  11 -->|output_file| 13;
  14["FastQC"];
  11 -->|output_file| 14;
  15["Replace"];
  12 -->|text_file| 15;
  16["FASTQ to FASTA"];
  13 -->|good_sequence_file| 16;
  17["FastQC"];
  13 -->|good_sequence_file| 17;
  18["Replace"];
  14 -->|text_file| 18;
  19["FASTA Width"];
  16 -->|output_file| 19;
  97f66112-d26f-4314-a4b4-29ed2d88e19c["Output\nSingle-end post quality control FASTA files"];
  19 --> 97f66112-d26f-4314-a4b4-29ed2d88e19c;
  style 97f66112-d26f-4314-a4b4-29ed2d88e19c stroke:#2c3143,stroke-width:4px;
  20["Replace"];
  17 -->|text_file| 20;
  21["MultiQC"];
  10 -->|outfile| 21;
  15 -->|outfile| 21;
  18 -->|outfile| 21;
  20 -->|outfile| 21;
  02fe7bec-eda7-408a-9373-e5e87f67232e["Output\nSingle-end MultiQC report"];
  21 --> 02fe7bec-eda7-408a-9373-e5e87f67232e;
  style 02fe7bec-eda7-408a-9373-e5e87f67232e stroke:#2c3143,stroke-width:4px;
  3785b661-05e3-431c-96c0-e34533ac1a5f["Output\nSingle-end MultiQC statistics"];
  21 --> 3785b661-05e3-431c-96c0-e34533ac1a5f;
  style 3785b661-05e3-431c-96c0-e34533ac1a5f stroke:#2c3143,stroke-width:4px;

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/mgnify-amplicon/workflows/mgnify-amplicon-pipeline-v5-quality-control-single-end.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