MGnify's amplicon pipeline v5.0 - ITS

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Collection\nLSU and SSU BED"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Collection\nProcessed sequences"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Filter empty datasets"];
  0 -->|output| 2;
  3["Extract element identifiers"];
  2 -->|output| 3;
  4["Filter collection"];
  3 -->|output| 4;
  1 -->|output| 4;
  5["bedtools MaskFastaBed"];
  4 -->|output_filtered| 5;
  2 -->|output| 5;
  ce25f1c3-97d5-499b-947a-4b624bcea4a7["Output\nITS FASTA files"];
  5 --> ce25f1c3-97d5-499b-947a-4b624bcea4a7;
  style ce25f1c3-97d5-499b-947a-4b624bcea4a7 stroke:#2c3143,stroke-width:4px;
  6["MAPseq"];
  5 -->|output| 6;
  7["MAPseq"];
  5 -->|output| 7;
  8["Text reformatting"];
  6 -->|classifications| 8;
  9["Text reformatting"];
  6 -->|otu_tsv| 9;
  10["Text reformatting"];
  6 -->|otu_tsv_notaxid| 10;
  11["Filter empty datasets"];
  6 -->|krona_format| 11;
  12["Text reformatting"];
  7 -->|classifications| 12;
  13["Text reformatting"];
  7 -->|otu_tsv| 13;
  14["Text reformatting"];
  7 -->|otu_tsv_notaxid| 14;
  15["Filter empty datasets"];
  7 -->|krona_format| 15;
  16["Filter empty datasets"];
  8 -->|outfile| 16;
  43b4ec81-612c-49ae-a8ee-a28e11c397df["Output\nITS taxonomic classifications using ITSoneDB"];
  16 --> 43b4ec81-612c-49ae-a8ee-a28e11c397df;
  style 43b4ec81-612c-49ae-a8ee-a28e11c397df stroke:#2c3143,stroke-width:4px;
  17["Filter empty datasets"];
  9 -->|outfile| 17;
  a430aea9-8530-4831-a6bd-d5e81d6df7e8["Output\nITS OTU tables (ITSoneDB)"];
  17 --> a430aea9-8530-4831-a6bd-d5e81d6df7e8;
  style a430aea9-8530-4831-a6bd-d5e81d6df7e8 stroke:#2c3143,stroke-width:4px;
  18["Filter empty datasets"];
  10 -->|outfile| 18;
  19["🛠️ Subworkflow\nMap empty/not empty collection to boolean "];
  style 19 fill:#edd,stroke:#900,stroke-width:4px;
  11 -->|output| 19;
  20["Filter empty datasets"];
  12 -->|outfile| 20;
  af0577e9-b1ae-406e-aba4-5b9c98d9434a["Output\nITS taxonomic classifications using UNITE DB"];
  20 --> af0577e9-b1ae-406e-aba4-5b9c98d9434a;
  style af0577e9-b1ae-406e-aba4-5b9c98d9434a stroke:#2c3143,stroke-width:4px;
  21["Filter empty datasets"];
  13 -->|outfile| 21;
  6ea84f46-6662-4875-ad8c-5137f863447a["Output\nITS OTU tables (UNITE DB)"];
  21 --> 6ea84f46-6662-4875-ad8c-5137f863447a;
  style 6ea84f46-6662-4875-ad8c-5137f863447a stroke:#2c3143,stroke-width:4px;
  22["Filter empty datasets"];
  14 -->|outfile| 22;
  23["🛠️ Subworkflow\nMap empty/not empty collection to boolean "];
  style 23 fill:#edd,stroke:#900,stroke-width:4px;
  15 -->|output| 23;
  24["🛠️ Subworkflow\nMap empty/not empty collection to boolean "];
  style 24 fill:#edd,stroke:#900,stroke-width:4px;
  18 -->|output| 24;
  25["Krona ITSoneDB"];
  11 -->|output| 25;
  19 -->|boolean_param| 25;
  07e569a7-d18e-4789-a1bf-74a90c2d70a2["Output\nITS taxonomic abundance pie charts (ITSoneDB)"];
  25 --> 07e569a7-d18e-4789-a1bf-74a90c2d70a2;
  style 07e569a7-d18e-4789-a1bf-74a90c2d70a2 stroke:#2c3143,stroke-width:4px;
  26["🛠️ Subworkflow\nMap empty/not empty collection to boolean "];
  style 26 fill:#edd,stroke:#900,stroke-width:4px;
  22 -->|output| 26;
  27["Krona ITS UNITE"];
  15 -->|output| 27;
  23 -->|boolean_param| 27;
  14132b74-67f7-4dba-a014-96508936a840["Output\nITS taxonomic abundance pie charts (UNITE DB)"];
  27 --> 14132b74-67f7-4dba-a014-96508936a840;
  style 14132b74-67f7-4dba-a014-96508936a840 stroke:#2c3143,stroke-width:4px;
  28["HDF5 ITSoneDB"];
  18 -->|output| 28;
  24 -->|boolean_param| 28;
  059ae843-53a0-4ed4-be61-6f8b0c4a1633["Output\nITS OTU tables in HDF5 format (ITSoneDB)"];
  28 --> 059ae843-53a0-4ed4-be61-6f8b0c4a1633;
  style 059ae843-53a0-4ed4-be61-6f8b0c4a1633 stroke:#2c3143,stroke-width:4px;
  29["JSON ITSoneDB"];
  18 -->|output| 29;
  24 -->|boolean_param| 29;
  874f05cb-81d2-4746-a3a6-20ebf4d511f6["Output\nITS OTU tables in JSON format (ITSoneDB)"];
  29 --> 874f05cb-81d2-4746-a3a6-20ebf4d511f6;
  style 874f05cb-81d2-4746-a3a6-20ebf4d511f6 stroke:#2c3143,stroke-width:4px;
  30["HDF5 ITS UNITE"];
  22 -->|output| 30;
  26 -->|boolean_param| 30;
  bf1abef3-2400-4985-8cb4-0bd0ae071fa6["Output\nITS OTU tables in HDF5 format (UNITE DB)"];
  30 --> bf1abef3-2400-4985-8cb4-0bd0ae071fa6;
  style bf1abef3-2400-4985-8cb4-0bd0ae071fa6 stroke:#2c3143,stroke-width:4px;
  31["JSON ITS UNITE"];
  22 -->|output| 31;
  26 -->|boolean_param| 31;
  39a261f1-34ae-4d54-86d2-4111374b1888["Output\nITS OTU tables in JSON format (UNITE DB)"];
  31 --> 39a261f1-34ae-4d54-86d2-4111374b1888;
  style 39a261f1-34ae-4d54-86d2-4111374b1888 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-its.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