Metatranscriptomics analysis using microbiome RNA-seq data - Workflow 3: Functional Information

Run Workflow in Galaxy

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• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Dataset\nInterleaced reads"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nTaxonomic profile"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["HUMAnN"];
  0 -->|output| 2;
  1 -->|output| 2;
  53259a06-0783-4db8-828e-328e7337f5b3["Output\nhumann_gene_families"];
  2 --> 53259a06-0783-4db8-828e-328e7337f5b3;
  style 53259a06-0783-4db8-828e-328e7337f5b3 stroke:#2c3143,stroke-width:4px;
  5aec39b6-317a-4fd0-b906-22d5a965e957["Output\nhumann_pathabundance"];
  2 --> 5aec39b6-317a-4fd0-b906-22d5a965e957;
  style 5aec39b6-317a-4fd0-b906-22d5a965e957 stroke:#2c3143,stroke-width:4px;
  3["Split a HUMAnN table"];
  2 -->|gene_families_tsv| 3;
  4["Regroup"];
  2 -->|gene_families_tsv| 4;
  5["Renormalize"];
  2 -->|gene_families_tsv| 5;
  4bd1c47e-66ac-41ff-bce9-51d0d86d2252["Output\nrenormalize_gene_families"];
  5 --> 4bd1c47e-66ac-41ff-bce9-51d0d86d2252;
  style 4bd1c47e-66ac-41ff-bce9-51d0d86d2252 stroke:#2c3143,stroke-width:4px;
  6["Rename features"];
  2 -->|gene_families_tsv| 6;
  7["Renormalize"];
  2 -->|pathabundance_tsv| 7;
  1715a5f6-3ac3-4ad2-a030-9307721e2b49["Output\nrenormalize_pathabundance"];
  7 --> 1715a5f6-3ac3-4ad2-a030-9307721e2b49;
  style 1715a5f6-3ac3-4ad2-a030-9307721e2b49 stroke:#2c3143,stroke-width:4px;
  8["Split a HUMAnN table"];
  2 -->|pathabundance_tsv| 8;
  9["Split a HUMAnN table"];
  4 -->|output| 9;
  10["Rename features"];
  4 -->|output| 10;
  11["Replace"];
  5 -->|output| 11;
  12["Unpack pathway abundances"];
  5 -->|output| 12;
  7 -->|output| 12;
  b24357e8-b6d3-4893-af63-ac4cf7494b33["Output\nunpack_pathway_abundance"];
  12 --> b24357e8-b6d3-4893-af63-ac4cf7494b33;
  style b24357e8-b6d3-4893-af63-ac4cf7494b33 stroke:#2c3143,stroke-width:4px;
  13["Select"];
  10 -->|output| 13;
  946a04fd-1854-4f08-8df1-1a3165651bae["Output\ncc_go"];
  13 --> 946a04fd-1854-4f08-8df1-1a3165651bae;
  style 946a04fd-1854-4f08-8df1-1a3165651bae stroke:#2c3143,stroke-width:4px;
  14["Select"];
  10 -->|output| 14;
  4f5f0597-39eb-42ce-8dd8-d920b52231c3["Output\nbp_go"];
  14 --> 4f5f0597-39eb-42ce-8dd8-d920b52231c3;
  style 4f5f0597-39eb-42ce-8dd8-d920b52231c3 stroke:#2c3143,stroke-width:4px;
  15["Select"];
  10 -->|output| 15;
  16["Split a HUMAnN table"];
  13 -->|out_file1| 16;
  17["Split a HUMAnN table"];
  14 -->|out_file1| 17;
  18["Sort"];
  15 -->|out_file1| 18;
  71abb759-b51f-4383-a791-27d8b1325e81["Output\nsorted_mf_go"];
  18 --> 71abb759-b51f-4383-a791-27d8b1325e81;
  style 71abb759-b51f-4383-a791-27d8b1325e81 stroke:#2c3143,stroke-width:4px;
  19["Split a HUMAnN table"];
  15 -->|out_file1| 19;

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/metatranscriptomics-short/workflows/workflow3_functional_information.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