Workflows

These workflows are associated with Clinical Metaproteiomics 1: Database-Generation

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.

WF1_Database_Generation_Workflow
Subina Mehta

Last updated Nov 21, 2024

Launch in Tutorial Mode
License: CC-BY-4.0
Tests: ❌ Results: Not yet automated

Download Galaxy Workflow.ga Galaxy Australia Galaxy Europe Galaxy France Galaxy Main Import to another server (≥23.0+ only!) 
flowchart TD
  0["ℹ️ Input Dataset\nHUMAN SwissProt Protein Database"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Collection\nInput MGF files Dataset Collection"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nSpecies_UniProt_FASTA"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nContaminants cRAP Protein Database "];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["Human UniProt Microbial Proteins cRAP for MetaNovo"];
  0 -->|output| 4;
  2 -->|output| 4;
  3 -->|output| 4;
  286f5bd4-fb0d-4649-8dac-f191acc72722["Output\nHuman UniProt Microbial Proteins cRAP for MetaNovo"];
  4 --> 286f5bd4-fb0d-4649-8dac-f191acc72722;
  style 286f5bd4-fb0d-4649-8dac-f191acc72722 stroke:#2c3143,stroke-width:4px;
  5["MetaNovo"];
  4 -->|output| 5;
  1 -->|output| 5;
  6["FASTA Merge Files and Filter Unique Sequences"];
  0 -->|output| 6;
  5 -->|output_fasta| 6;
  3 -->|output| 6;
  de57cd9d-ac05-4397-9d44-e65620913447["Output\nHuman UniProt Microbial Proteins (from MetaNovo) and cRAP "];
  6 --> de57cd9d-ac05-4397-9d44-e65620913447;
  style de57cd9d-ac05-4397-9d44-e65620913447 stroke:#2c3143,stroke-width:4px;

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
  • Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
  • Click on Import at the top-right of the screen
  • 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”
  • 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