MGnify's amplicon pipeline v5.0 - rRNA prediction

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Collection\nProcessed sequences"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nClan information file"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["cmsearch"];
  0 -->|output| 2;
  3["Filter empty datasets"];
  2 -->|outfile| 3;
  4["CMsearch deoverlap"];
  1 -->|output| 4;
  3 -->|output| 4;
  5["Query Tabular"];
  4 -->|deoverlapped_matches| 5;
  6["SSU BED forward"];
  5 -->|output| 6;
  7["SSU BED reverse"];
  5 -->|output1| 7;
  8["LSU BED forward"];
  5 -->|output2| 8;
  9["LSU BED reverse"];
  5 -->|output3| 9;
  10["SSU BED"];
  6 -->|outfile| 10;
  7 -->|outfile| 10;
  11["LSU BED"];
  8 -->|outfile| 11;
  9 -->|outfile| 11;
  12["Filter empty datasets"];
  10 -->|output| 12;
  13["Filter empty datasets"];
  11 -->|output| 13;
  14["Concatenate"];
  10 -->|output| 14;
  11 -->|output| 14;
  61df13ed-4ffa-42b8-af91-b13d72d4a5fe["Output\nLSU and SSU BED regions"];
  14 --> 61df13ed-4ffa-42b8-af91-b13d72d4a5fe;
  style 61df13ed-4ffa-42b8-af91-b13d72d4a5fe stroke:#2c3143,stroke-width:4px;
  15["Extract element identifiers"];
  12 -->|output| 15;
  16["Extract element identifiers"];
  13 -->|output| 16;
  17["Filter collection"];
  15 -->|output| 17;
  0 -->|output| 17;
  18["Filter collection"];
  16 -->|output| 18;
  0 -->|output| 18;
  19["bedtools getfasta"];
  17 -->|output_filtered| 19;
  12 -->|output| 19;
  20["bedtools getfasta"];
  18 -->|output_filtered| 20;
  13 -->|output| 20;
  21["FASTA Width"];
  19 -->|output| 21;
  a5040877-43f1-4942-b2de-404c98bac842["Output\nSSU FASTA files"];
  21 --> a5040877-43f1-4942-b2de-404c98bac842;
  style a5040877-43f1-4942-b2de-404c98bac842 stroke:#2c3143,stroke-width:4px;
  22["FASTA Width"];
  20 -->|output| 22;
  2cc6ed90-b1f0-438f-8cfe-1a4877295079["Output\nLSU FASTA files"];
  22 --> 2cc6ed90-b1f0-438f-8cfe-1a4877295079;
  style 2cc6ed90-b1f0-438f-8cfe-1a4877295079 stroke:#2c3143,stroke-width:4px;
  23["MAPseq"];
  21 -->|output| 23;
  24["MAPseq"];
  22 -->|output| 24;
  25["Text reformatting"];
  23 -->|classifications| 25;
  26["Text reformatting"];
  23 -->|otu_tsv| 26;
  27["Text reformatting"];
  23 -->|otu_tsv_notaxid| 27;
  28["Filter empty datasets"];
  23 -->|krona_format| 28;
  29["Text reformatting"];
  24 -->|classifications| 29;
  30["Text reformatting"];
  24 -->|otu_tsv| 30;
  31["Text reformatting"];
  24 -->|otu_tsv_notaxid| 31;
  32["Filter empty datasets"];
  24 -->|krona_format| 32;
  33["Filter empty datasets"];
  25 -->|outfile| 33;
  2f42bcff-aeba-4628-9f36-d7f564b39de3["Output\nSSU taxonomic classifications using SILVA DB"];
  33 --> 2f42bcff-aeba-4628-9f36-d7f564b39de3;
  style 2f42bcff-aeba-4628-9f36-d7f564b39de3 stroke:#2c3143,stroke-width:4px;
  34["Filter empty datasets"];
  26 -->|outfile| 34;
  646eda6d-d954-40b7-a4f0-c4ce1346e239["Output\nSSU OTU tables (SILVA DB)"];
  34 --> 646eda6d-d954-40b7-a4f0-c4ce1346e239;
  style 646eda6d-d954-40b7-a4f0-c4ce1346e239 stroke:#2c3143,stroke-width:4px;
  35["Filter empty datasets"];
  27 -->|outfile| 35;
  36["🛠️ Subworkflow\nMap empty/not empty collection to boolean "];
  style 36 fill:#edd,stroke:#900,stroke-width:4px;
  28 -->|output| 36;
  37["Filter empty datasets"];
  29 -->|outfile| 37;
  0e6e5501-7a4f-409c-b595-b0481946e3ca["Output\nLSU taxonomic classifications using SILVA DB"];
  37 --> 0e6e5501-7a4f-409c-b595-b0481946e3ca;
  style 0e6e5501-7a4f-409c-b595-b0481946e3ca stroke:#2c3143,stroke-width:4px;
  38["Filter empty datasets"];
  30 -->|outfile| 38;
  2447fb7e-a135-4c0d-8804-9d10c2247529["Output\nLSU OTU tables (SILVA DB)"];
  38 --> 2447fb7e-a135-4c0d-8804-9d10c2247529;
  style 2447fb7e-a135-4c0d-8804-9d10c2247529 stroke:#2c3143,stroke-width:4px;
  39["Filter empty datasets"];
  31 -->|outfile| 39;
  40["🛠️ Subworkflow\nMap empty/not empty collection to boolean "];
  style 40 fill:#edd,stroke:#900,stroke-width:4px;
  32 -->|output| 40;
  41["🛠️ Subworkflow\nMap empty/not empty collection to boolean "];
  style 41 fill:#edd,stroke:#900,stroke-width:4px;
  35 -->|output| 41;
  42["Krona SSU SILVA"];
  28 -->|output| 42;
  36 -->|boolean_param| 42;
  fe12c8ea-82e8-413c-95ad-1805495ae6fb["Output\nSSU taxonomic abundance pie charts (SILVA DB)"];
  42 --> fe12c8ea-82e8-413c-95ad-1805495ae6fb;
  style fe12c8ea-82e8-413c-95ad-1805495ae6fb stroke:#2c3143,stroke-width:4px;
  43["🛠️ Subworkflow\nMap empty/not empty collection to boolean "];
  style 43 fill:#edd,stroke:#900,stroke-width:4px;
  39 -->|output| 43;
  44["Krona LSU SILVA"];
  32 -->|output| 44;
  40 -->|boolean_param| 44;
  86cf82e3-e3f3-47d5-a816-f55464a7e421["Output\nLSU taxonomic abundance pie charts (SILVA DB)"];
  44 --> 86cf82e3-e3f3-47d5-a816-f55464a7e421;
  style 86cf82e3-e3f3-47d5-a816-f55464a7e421 stroke:#2c3143,stroke-width:4px;
  45["HDF5 SSU SILVA"];
  35 -->|output| 45;
  41 -->|boolean_param| 45;
  4dd647f3-b100-426b-b95d-c0793f8f9d55["Output\nSSU OTU tables in HDF5 format (SILVA DB)"];
  45 --> 4dd647f3-b100-426b-b95d-c0793f8f9d55;
  style 4dd647f3-b100-426b-b95d-c0793f8f9d55 stroke:#2c3143,stroke-width:4px;
  46["JSON SSU SILVA"];
  35 -->|output| 46;
  41 -->|boolean_param| 46;
  87281088-3c07-46bb-8cf8-c1b3bc882a4a["Output\nSSU OTU tables in JSON format (SILVA DB)"];
  46 --> 87281088-3c07-46bb-8cf8-c1b3bc882a4a;
  style 87281088-3c07-46bb-8cf8-c1b3bc882a4a stroke:#2c3143,stroke-width:4px;
  47["HDF5 LSU SILVA"];
  39 -->|output| 47;
  43 -->|boolean_param| 47;
  48da1567-b17d-473f-96c1-d137073f6d12["Output\nLSU OTU tables in HDF5 format (SILVA DB)"];
  47 --> 48da1567-b17d-473f-96c1-d137073f6d12;
  style 48da1567-b17d-473f-96c1-d137073f6d12 stroke:#2c3143,stroke-width:4px;
  48["JSON LSU SILVA"];
  39 -->|output| 48;
  43 -->|boolean_param| 48;
  5d5b34f6-6f44-4bad-bd38-ecb70ccc3451["Output\nLSU OTU tables in JSON format (SILVA DB)"];
  48 --> 5d5b34f6-6f44-4bad-bd38-ecb70ccc3451;
  style 5d5b34f6-6f44-4bad-bd38-ecb70ccc3451 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-rrna-prediction.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