MGnify's amplicon pipeline v5.0

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nSRA accession list"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nClan information file"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Parameter\nTrimmomatic sliding window number of bases to average across"];
  style 2 fill:#ded,stroke:#393,stroke-width:4px;
  3["ℹ️ Input Parameter\nTrimmomatic sliding window average quality"];
  style 3 fill:#ded,stroke:#393,stroke-width:4px;
  4["ℹ️ Input Parameter\nPE fastp - Enable base correction"];
  style 4 fill:#ded,stroke:#393,stroke-width:4px;
  5["ℹ️ Input Parameter\nTrimmomatic leading"];
  style 5 fill:#ded,stroke:#393,stroke-width:4px;
  6["ℹ️ Input Parameter\nPE fastp - Qualified quality phred"];
  style 6 fill:#ded,stroke:#393,stroke-width:4px;
  7["ℹ️ Input Parameter\nTrimmomatic trailing"];
  style 7 fill:#ded,stroke:#393,stroke-width:4px;
  8["ℹ️ Input Parameter\nPE fastp - Unqualified percent limit "];
  style 8 fill:#ded,stroke:#393,stroke-width:4px;
  9["ℹ️ Input Parameter\nTrimmomatic min length"];
  style 9 fill:#ded,stroke:#393,stroke-width:4px;
  10["ℹ️ Input Parameter\nPE fastp - Length required"];
  style 10 fill:#ded,stroke:#393,stroke-width:4px;
  11["ℹ️ Input Parameter\nLength filtering minimum size"];
  style 11 fill:#ded,stroke:#393,stroke-width:4px;
  12["ℹ️ Input Parameter\nAmbiguity filtering maximal N percentage threshold to conserve sequences"];
  style 12 fill:#ded,stroke:#393,stroke-width:4px;
  13["ℹ️ Input Parameter\nSSU taxonomic abundance summary table name"];
  style 13 fill:#ded,stroke:#393,stroke-width:4px;
  14["ℹ️ Input Parameter\nSSU phylum level taxonomic abundance summary table name"];
  style 14 fill:#ded,stroke:#393,stroke-width:4px;
  15["ℹ️ Input Parameter\nLSU taxonomic abundance summary table name"];
  style 15 fill:#ded,stroke:#393,stroke-width:4px;
  16["ℹ️ Input Parameter\nLSU phylum level taxonomic abundance summary table name"];
  style 16 fill:#ded,stroke:#393,stroke-width:4px;
  17["ℹ️ Input Parameter\nITSoneDB taxonomic abundance summary table name"];
  style 17 fill:#ded,stroke:#393,stroke-width:4px;
  18["ℹ️ Input Parameter\nITSoneDB phylum level taxonomic abundance summary table name"];
  style 18 fill:#ded,stroke:#393,stroke-width:4px;
  19["ℹ️ Input Parameter\nITS UNITE DB taxonomic abundance summary table name"];
  style 19 fill:#ded,stroke:#393,stroke-width:4px;
  20["ℹ️ Input Parameter\nITS UNITE DB phylum level taxonomic abundance summary table name"];
  style 20 fill:#ded,stroke:#393,stroke-width:4px;
  21["fastq-dl"];
  0 -->|output| 21;
  22["Convert compressed file to uncompressed."];
  21 -->|single_end_collection| 22;
  23["Convert compressed file to uncompressed."];
  21 -->|paired_end_collection| 23;
  24["Text reformatting"];
  22 -->|output1| 24;
  25["Text reformatting"];
  23 -->|output1| 25;
  26["Convert uncompressed file to compressed"];
  24 -->|outfile| 26;
  27["Convert uncompressed file to compressed"];
  25 -->|outfile| 27;
  28["🛠️ Subworkflow\nMGnify’s amplicon pipeline v5.0 - Quality control SE"];
  style 28 fill:#edd,stroke:#900,stroke-width:4px;
  12 -->|output| 28;
  11 -->|output| 28;
  26 -->|output1| 28;
  5 -->|output| 28;
  9 -->|output| 28;
  3 -->|output| 28;
  2 -->|output| 28;
  7 -->|output| 28;
  6f6ecd17-f506-4c5e-b872-a1b79620e44c["Output\nSingle-end MultiQC report"];
  28 --> 6f6ecd17-f506-4c5e-b872-a1b79620e44c;
  style 6f6ecd17-f506-4c5e-b872-a1b79620e44c stroke:#2c3143,stroke-width:4px;
  8cf887ba-467f-4192-9eba-29cb8c7a5a1a["Output\nSingle-end post quality control FASTA files"];
  28 --> 8cf887ba-467f-4192-9eba-29cb8c7a5a1a;
  style 8cf887ba-467f-4192-9eba-29cb8c7a5a1a stroke:#2c3143,stroke-width:4px;
  91c6c565-ca5b-4f23-ba15-40ab9378837d["Output\nSingle-end MultiQC statistics"];
  28 --> 91c6c565-ca5b-4f23-ba15-40ab9378837d;
  style 91c6c565-ca5b-4f23-ba15-40ab9378837d stroke:#2c3143,stroke-width:4px;
  29["🛠️ Subworkflow\nMGnify’s amplicon pipeline v5.0 - Quality control PE"];
  style 29 fill:#edd,stroke:#900,stroke-width:4px;
  12 -->|output| 29;
  11 -->|output| 29;
  27 -->|output1| 29;
  5 -->|output| 29;
  9 -->|output| 29;
  3 -->|output| 29;
  2 -->|output| 29;
  7 -->|output| 29;
  4 -->|output| 29;
  10 -->|output| 29;
  6 -->|output| 29;
  8 -->|output| 29;
  fd1bad4c-912f-4fb3-9dbf-44abf4fad5d6["Output\nPaired-end MultiQC report"];
  29 --> fd1bad4c-912f-4fb3-9dbf-44abf4fad5d6;
  style fd1bad4c-912f-4fb3-9dbf-44abf4fad5d6 stroke:#2c3143,stroke-width:4px;
  2c08c132-f9c7-49b2-b4f3-1ecc424e1254["Output\nPaired-end post quality control FASTA files"];
  29 --> 2c08c132-f9c7-49b2-b4f3-1ecc424e1254;
  style 2c08c132-f9c7-49b2-b4f3-1ecc424e1254 stroke:#2c3143,stroke-width:4px;
  64f4d25d-2f9c-41d2-9a05-d31e010307f4["Output\nPaired-end MultiQC statistics"];
  29 --> 64f4d25d-2f9c-41d2-9a05-d31e010307f4;
  style 64f4d25d-2f9c-41d2-9a05-d31e010307f4 stroke:#2c3143,stroke-width:4px;
  30["Merge collections"];
  28 -->|Single-end post quality control FASTA files| 30;
  29 -->|Paired-end post quality control FASTA files| 30;
  31["🛠️ Subworkflow\nMGnify’s amplicon pipeline v5.0 - rRNA prediction"];
  style 31 fill:#edd,stroke:#900,stroke-width:4px;
  1 -->|output| 31;
  30 -->|output| 31;
  d1088f04-9e2f-416d-9dfc-87ab5c3d8652["Output\nSSU FASTA files"];
  31 --> d1088f04-9e2f-416d-9dfc-87ab5c3d8652;
  style d1088f04-9e2f-416d-9dfc-87ab5c3d8652 stroke:#2c3143,stroke-width:4px;
  8af9c378-2a91-4339-93eb-743376bceb78["Output\nSSU OTU tables in HDF5 format (SILVA DB)"];
  31 --> 8af9c378-2a91-4339-93eb-743376bceb78;
  style 8af9c378-2a91-4339-93eb-743376bceb78 stroke:#2c3143,stroke-width:4px;
  46ede89c-7a3c-423d-9dbb-3b75b7faf55d["Output\nSSU taxonomic abundance pie charts (SILVA DB)"];
  31 --> 46ede89c-7a3c-423d-9dbb-3b75b7faf55d;
  style 46ede89c-7a3c-423d-9dbb-3b75b7faf55d stroke:#2c3143,stroke-width:4px;
  36d3f861-4728-409f-9980-fd0d3cbe0361["Output\nSSU OTU tables in JSON format (SILVA DB)"];
  31 --> 36d3f861-4728-409f-9980-fd0d3cbe0361;
  style 36d3f861-4728-409f-9980-fd0d3cbe0361 stroke:#2c3143,stroke-width:4px;
  c321a9ab-fc6a-47b7-96a2-5e169d55012e["Output\nLSU taxonomic abundance pie charts (SILVA DB)"];
  31 --> c321a9ab-fc6a-47b7-96a2-5e169d55012e;
  style c321a9ab-fc6a-47b7-96a2-5e169d55012e stroke:#2c3143,stroke-width:4px;
  51d11ea0-8014-4488-a037-5430f62714ba["Output\nLSU OTU tables in HDF5 format (SILVA DB)"];
  31 --> 51d11ea0-8014-4488-a037-5430f62714ba;
  style 51d11ea0-8014-4488-a037-5430f62714ba stroke:#2c3143,stroke-width:4px;
  0c0f64de-8be5-4517-8566-e3b1fda38458["Output\nLSU FASTA files"];
  31 --> 0c0f64de-8be5-4517-8566-e3b1fda38458;
  style 0c0f64de-8be5-4517-8566-e3b1fda38458 stroke:#2c3143,stroke-width:4px;
  89e4f49b-1e0a-4bdf-98d7-5a3b99204d3a["Output\nLSU OTU tables in JSON format (SILVA DB)"];
  31 --> 89e4f49b-1e0a-4bdf-98d7-5a3b99204d3a;
  style 89e4f49b-1e0a-4bdf-98d7-5a3b99204d3a stroke:#2c3143,stroke-width:4px;
  73b814b6-9da1-47d8-85ed-72d10b2a4314["Output\nLSU taxonomic classifications using SILVA DB"];
  31 --> 73b814b6-9da1-47d8-85ed-72d10b2a4314;
  style 73b814b6-9da1-47d8-85ed-72d10b2a4314 stroke:#2c3143,stroke-width:4px;
  2ce160a6-8d19-4b83-a68d-1975f60d42fe["Output\nLSU and SSU BED regions"];
  31 --> 2ce160a6-8d19-4b83-a68d-1975f60d42fe;
  style 2ce160a6-8d19-4b83-a68d-1975f60d42fe stroke:#2c3143,stroke-width:4px;
  9f6eeabf-d2de-4c91-bf1c-167221e0d233["Output\nSSU OTU tables (SILVA DB)"];
  31 --> 9f6eeabf-d2de-4c91-bf1c-167221e0d233;
  style 9f6eeabf-d2de-4c91-bf1c-167221e0d233 stroke:#2c3143,stroke-width:4px;
  5f1081b1-9df2-422b-9ba9-48b4f219f892["Output\nSSU taxonomic classifications using SILVA DB"];
  31 --> 5f1081b1-9df2-422b-9ba9-48b4f219f892;
  style 5f1081b1-9df2-422b-9ba9-48b4f219f892 stroke:#2c3143,stroke-width:4px;
  ef19d94e-c4da-4ede-842e-54104811ac2e["Output\nLSU OTU tables (SILVA DB)"];
  31 --> ef19d94e-c4da-4ede-842e-54104811ac2e;
  style ef19d94e-c4da-4ede-842e-54104811ac2e stroke:#2c3143,stroke-width:4px;
  32["🛠️ Subworkflow\nMGnify’s amplicon pipeline v5.0 - ITS"];
  style 32 fill:#edd,stroke:#900,stroke-width:4px;
  31 -->|LSU and SSU BED regions| 32;
  30 -->|output| 32;
  39a4794a-5298-4206-b06d-c79b2fb4c423["Output\nITS OTU tables in HDF5 format (ITSoneDB)"];
  32 --> 39a4794a-5298-4206-b06d-c79b2fb4c423;
  style 39a4794a-5298-4206-b06d-c79b2fb4c423 stroke:#2c3143,stroke-width:4px;
  167efccc-7370-40ef-b9c2-356c637259cd["Output\nITS taxonomic abundance pie charts (UNITE DB)"];
  32 --> 167efccc-7370-40ef-b9c2-356c637259cd;
  style 167efccc-7370-40ef-b9c2-356c637259cd stroke:#2c3143,stroke-width:4px;
  22b09e00-6c88-4894-8000-d8ecebe51cb9["Output\nITS taxonomic classifications using ITSoneDB"];
  32 --> 22b09e00-6c88-4894-8000-d8ecebe51cb9;
  style 22b09e00-6c88-4894-8000-d8ecebe51cb9 stroke:#2c3143,stroke-width:4px;
  825fc92e-513e-4672-9b03-8a509b753189["Output\nITS OTU tables in JSON format (ITSoneDB)"];
  32 --> 825fc92e-513e-4672-9b03-8a509b753189;
  style 825fc92e-513e-4672-9b03-8a509b753189 stroke:#2c3143,stroke-width:4px;
  a5342c91-63e9-4aa8-88ef-9ad9ddc0ac05["Output\nITS OTU tables in HDF5 format (UNITE DB)"];
  32 --> a5342c91-63e9-4aa8-88ef-9ad9ddc0ac05;
  style a5342c91-63e9-4aa8-88ef-9ad9ddc0ac05 stroke:#2c3143,stroke-width:4px;
  3e8e45f5-c8b9-4cc0-b759-d5911e4b0a1f["Output\nITS OTU tables in JSON format (UNITE DB)"];
  32 --> 3e8e45f5-c8b9-4cc0-b759-d5911e4b0a1f;
  style 3e8e45f5-c8b9-4cc0-b759-d5911e4b0a1f stroke:#2c3143,stroke-width:4px;
  ce1cc3a7-d9f1-43e9-9a29-bf323538f003["Output\nITS OTU tables (UNITE DB)"];
  32 --> ce1cc3a7-d9f1-43e9-9a29-bf323538f003;
  style ce1cc3a7-d9f1-43e9-9a29-bf323538f003 stroke:#2c3143,stroke-width:4px;
  6d44ec4c-ddc1-4d8f-a4e6-e7da84fca0d0["Output\nITS FASTA files"];
  32 --> 6d44ec4c-ddc1-4d8f-a4e6-e7da84fca0d0;
  style 6d44ec4c-ddc1-4d8f-a4e6-e7da84fca0d0 stroke:#2c3143,stroke-width:4px;
  624858b8-dde6-4d8e-894e-3a32732ce588["Output\nITS taxonomic abundance pie charts (ITSoneDB)"];
  32 --> 624858b8-dde6-4d8e-894e-3a32732ce588;
  style 624858b8-dde6-4d8e-894e-3a32732ce588 stroke:#2c3143,stroke-width:4px;
  9cdce277-457d-4c19-823a-108876f42463["Output\nITS OTU tables (ITSoneDB)"];
  32 --> 9cdce277-457d-4c19-823a-108876f42463;
  style 9cdce277-457d-4c19-823a-108876f42463 stroke:#2c3143,stroke-width:4px;
  332b291c-1b05-4762-b021-47cb65ba7673["Output\nITS taxonomic classifications using UNITE DB"];
  32 --> 332b291c-1b05-4762-b021-47cb65ba7673;
  style 332b291c-1b05-4762-b021-47cb65ba7673 stroke:#2c3143,stroke-width:4px;
  33["🛠️ Subworkflow\nMap empty/not empty collection to boolean "];
  style 33 fill:#edd,stroke:#900,stroke-width:4px;
  31 -->|SSU OTU tables SILVA DB| 33;
  34["🛠️ Subworkflow\nMap empty/not empty collection to boolean "];
  style 34 fill:#edd,stroke:#900,stroke-width:4px;
  31 -->|LSU OTU tables SILVA DB| 34;
  35["🛠️ Subworkflow\nMap empty/not empty collection to boolean "];
  style 35 fill:#edd,stroke:#900,stroke-width:4px;
  32 -->|ITS OTU tables ITSoneDB| 35;
  36["🛠️ Subworkflow\nMap empty/not empty collection to boolean "];
  style 36 fill:#edd,stroke:#900,stroke-width:4px;
  32 -->|ITS OTU tables UNITE DB| 36;
  37["🛠️ Subworkflow\nMGnify amplicon summary tables"];
  style 37 fill:#edd,stroke:#900,stroke-width:4px;
  31 -->|SSU OTU tables SILVA DB| 37;
  14 -->|output| 37;
  13 -->|output| 37;
  33 -->|boolean_param| 37;
  627a3fc8-2a61-4096-892d-fcebc1a788b4["Output\nSSU phylum level taxonomic abundance summary table"];
  37 --> 627a3fc8-2a61-4096-892d-fcebc1a788b4;
  style 627a3fc8-2a61-4096-892d-fcebc1a788b4 stroke:#2c3143,stroke-width:4px;
  8b025e65-0071-4994-ab77-2c10252ba471["Output\nSSU taxonomic abundance summary table"];
  37 --> 8b025e65-0071-4994-ab77-2c10252ba471;
  style 8b025e65-0071-4994-ab77-2c10252ba471 stroke:#2c3143,stroke-width:4px;
  38["🛠️ Subworkflow\nMGnify amplicon summary tables"];
  style 38 fill:#edd,stroke:#900,stroke-width:4px;
  31 -->|LSU OTU tables SILVA DB| 38;
  16 -->|output| 38;
  15 -->|output| 38;
  34 -->|boolean_param| 38;
  11d82afa-e60a-4da2-9745-39b19e3d653a["Output\nLSU phylum level taxonomic abundance summary table"];
  38 --> 11d82afa-e60a-4da2-9745-39b19e3d653a;
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  99c9ae4c-f816-4569-9a44-7884c9c5550e["Output\nLSU taxonomic abundance summary table"];
  38 --> 99c9ae4c-f816-4569-9a44-7884c9c5550e;
  style 99c9ae4c-f816-4569-9a44-7884c9c5550e stroke:#2c3143,stroke-width:4px;
  39["🛠️ Subworkflow\nITSoneDB summary tables"];
  style 39 fill:#edd,stroke:#900,stroke-width:4px;
  32 -->|ITS OTU tables ITSoneDB| 39;
  18 -->|output| 39;
  17 -->|output| 39;
  35 -->|boolean_param| 39;
  5b61f997-1cd1-496b-b0fd-d3a98e130e66["Output\nITSoneDB taxonomic abundance summary table"];
  39 --> 5b61f997-1cd1-496b-b0fd-d3a98e130e66;
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  f3080e71-83a2-4cad-9ddf-9b0f806af898["Output\nITSoneDB phylum level taxonomic abundance summary table"];
  39 --> f3080e71-83a2-4cad-9ddf-9b0f806af898;
  style f3080e71-83a2-4cad-9ddf-9b0f806af898 stroke:#2c3143,stroke-width:4px;
  40["🛠️ Subworkflow\nUNITE summary tables"];
  style 40 fill:#edd,stroke:#900,stroke-width:4px;
  32 -->|ITS OTU tables UNITE DB| 40;
  20 -->|output| 40;
  19 -->|output| 40;
  36 -->|boolean_param| 40;
  5d0937ff-5bb2-458d-9cf6-85096119c089["Output\nITS UNITE DB phylum level taxonomic abundance summary table"];
  40 --> 5d0937ff-5bb2-458d-9cf6-85096119c089;
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  84ee23b4-9c6c-4ee2-b71a-6412be55c1e3["Output\nITS UNITE DB taxonomic abundance summary table"];
  40 --> 84ee23b4-9c6c-4ee2-b71a-6412be55c1e3;
  style 84ee23b4-9c6c-4ee2-b71a-6412be55c1e3 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-complete.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