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

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Collection\nPaired-end reads"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Parameter\nfastp - Enable base correction"];
  style 1 fill:#ded,stroke:#393,stroke-width:4px;
  2["ℹ️ Input Parameter\nfastp - Qualified quality phred"];
  style 2 fill:#ded,stroke:#393,stroke-width:4px;
  3["ℹ️ Input Parameter\nfastp - Unqualified percent limit "];
  style 3 fill:#ded,stroke:#393,stroke-width:4px;
  4["ℹ️ Input Parameter\nfastp - Length required"];
  style 4 fill:#ded,stroke:#393,stroke-width:4px;
  5["ℹ️ Input Parameter\nTrimmomatic - SLIDINGWINDOW - Number of bases to average across"];
  style 5 fill:#ded,stroke:#393,stroke-width:4px;
  6["ℹ️ Input Parameter\nTrimmomatic - SLIDINGWINDOW - Average quality required"];
  style 6 fill:#ded,stroke:#393,stroke-width:4px;
  7["ℹ️ Input Parameter\nTrimmomatic - LEADING"];
  style 7 fill:#ded,stroke:#393,stroke-width:4px;
  8["ℹ️ Input Parameter\nTrimmomatic - TRAILING"];
  style 8 fill:#ded,stroke:#393,stroke-width:4px;
  9["ℹ️ Input Parameter\nLength filtering - Minimum size"];
  style 9 fill:#ded,stroke:#393,stroke-width:4px;
  10["ℹ️ Input Parameter\nTrimmomatic - MINLEN"];
  style 10 fill:#ded,stroke:#393,stroke-width:4px;
  11["ℹ️ Input Parameter\nAmbiguity filtering - Maximal N percentage threshold to conserve sequences"];
  style 11 fill:#ded,stroke:#393,stroke-width:4px;
  12["fastp"];
  4 -->|output| 12;
  2 -->|output| 12;
  3 -->|output| 12;
  1 -->|output| 12;
  0 -->|output| 12;
  13["Unzip collection"];
  12 -->|output_paired_coll| 13;
  14["Merging paired-end Illumina reads SeqPrep, modified for use with MGnify piplines"];
  13 -->|forward| 14;
  13 -->|reverse| 14;
  15["Trimming"];
  6 -->|output| 15;
  5 -->|output| 15;
  7 -->|output| 15;
  8 -->|output| 15;
  10 -->|output| 15;
  14 -->|merged| 15;
  16["FastQC"];
  14 -->|merged| 16;
  17["Length filtering"];
  15 -->|fastq_out| 17;
  9 -->|output| 17;
  18["FastQC"];
  15 -->|fastq_out| 18;
  19["Replace"];
  16 -->|text_file| 19;
  20["Ambiguity filtering"];
  11 -->|output| 20;
  17 -->|output_file| 20;
  21["FastQC"];
  17 -->|output_file| 21;
  22["Replace"];
  18 -->|text_file| 22;
  23["FASTQ to FASTA"];
  20 -->|good_sequence_file| 23;
  24["FastQC"];
  20 -->|good_sequence_file| 24;
  25["Replace"];
  21 -->|text_file| 25;
  26["FASTA Width"];
  23 -->|output_file| 26;
  05008f5e-c45d-4346-8e85-ec2fb5877a95["Output\nPaired-end post quality control FASTA files"];
  26 --> 05008f5e-c45d-4346-8e85-ec2fb5877a95;
  style 05008f5e-c45d-4346-8e85-ec2fb5877a95 stroke:#2c3143,stroke-width:4px;
  27["Replace"];
  24 -->|text_file| 27;
  28["MultiQC"];
  19 -->|outfile| 28;
  22 -->|outfile| 28;
  25 -->|outfile| 28;
  27 -->|outfile| 28;
  82fc1b1a-80b4-4abf-8150-cca1d82337bb["Output\nPaired-end MultiQC report"];
  28 --> 82fc1b1a-80b4-4abf-8150-cca1d82337bb;
  style 82fc1b1a-80b4-4abf-8150-cca1d82337bb stroke:#2c3143,stroke-width:4px;
  6b214cd1-fd0b-4d57-89f4-5758e4ad0c32["Output\nPaired-end MultiQC statistics"];
  28 --> 6b214cd1-fd0b-4d57-89f4-5758e4ad0c32;
  style 6b214cd1-fd0b-4d57-89f4-5758e4ad0c32 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-paired-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