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

microbiome-mgnify-amplicon/mgnify-amplicon-pipeline-v5-quality-control-paired-end

Author(s)
EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep
version Version
1
last_modification Last updated
Jul 30, 2025
license License
Apache-2.0
galaxy-tags Tags
MGnify_Amplicon
amplicon
metagenomics
name:microgalaxy

Features
Tutorial
hands_on MGnify v5.0 Amplicon Pipeline
workflow Other workflows associated with this material
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:
RO-Crate logo with flask Download Workflow RO-Crate
Launch in Tutorial Mode question
galaxy-download Download
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

Input Label
Input dataset collection Paired-end reads
Input parameter fastp - Enable base correction
Input parameter fastp - Qualified quality phred
Input parameter fastp - Unqualified percent limit
Input parameter fastp - Length required
Input parameter Trimmomatic - SLIDINGWINDOW - Number of bases to average across
Input parameter Trimmomatic - SLIDINGWINDOW - Average quality required
Input parameter Trimmomatic - LEADING
Input parameter Trimmomatic - TRAILING
Input parameter Length filtering - Minimum size
Input parameter Trimmomatic - MINLEN
Input parameter Ambiguity filtering - Maximal N percentage threshold to conserve sequences

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.1+galaxy2 FASTA Width
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3 MultiQC

Tools

Tool Links
__UNZIP_COLLECTION__
toolshed.g2.bx.psu.edu/repos/bgruening/mgnify_seqprep/mgnify_seqprep/1.2+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.1+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.5+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/prinseq/prinseq/0.20.4+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.39+galaxy2 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
  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:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
1 0125a7f84 2025-07-30 12:59:47 remove version from folder name for future-proofness

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