Workflows

These workflows are associated with Analyse HeLa fluorescence siRNA screen

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.

analyze_screen
Till Korten

Last updated Nov 8, 2023

Launch in Tutorial Mode question
License: MIT
Tests: ✅ Results: Not yet automated

flowchart TD
  0["ℹ️ Input Collection\ninput images"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nrules"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["🛠️ Subworkflow\nfeature_extraction"];
  style 2 fill:#edd,stroke:#900,stroke-width:4px;
  0 -->|output| 2;
  1 -->|output| 2;
  3["merge_table"];
  2 -->|output| 3;
  3fc2324d-233b-4785-9fb7-9c30b2daaef4["Output\noutput"];
  3 --> 3fc2324d-233b-4785-9fb7-9c30b2daaef4;
  style 3fc2324d-233b-4785-9fb7-9c30b2daaef4 stroke:#2c3143,stroke-width:4px;
	
feature_extraction
Till Korten

Last updated Nov 8, 2023

Launch in Tutorial Mode question
License: MIT
Tests: ✅ Results: Not yet automated

flowchart TD
  0["ℹ️ Input Dataset\ninput image"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nrules"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Filter Image"];
  0 -->|output| 2;
  3["Auto Threshold"];
  2 -->|output| 3;
  4["Split objects"];
  3 -->|output| 4;
  5["2D Feature Extraction"];
  4 -->|output| 5;
  6["Filter segmentation"];
  5 -->|output| 6;
  4 -->|output| 6;
  1 -->|output| 6;
  b90cbc94-33fd-4600-96b5-8cf0bcaf2e94["Output\noutput"];
  6 --> b90cbc94-33fd-4600-96b5-8cf0bcaf2e94;
  style b90cbc94-33fd-4600-96b5-8cf0bcaf2e94 stroke:#2c3143,stroke-width:4px;
  7["2D Feature Extraction"];
  6 -->|output| 7;
  0 -->|output| 7;
  3d3c037a-50ef-443b-a6f8-8a37db6bfb36["Output\noutput"];
  7 --> 3d3c037a-50ef-443b-a6f8-8a37db6bfb36;
  style 3d3c037a-50ef-443b-a6f8-8a37db6bfb36 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 galaxy-upload 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