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.

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;
  1 -->|output| 2;
  0 -->|output| 2;
  3["Collapse Collection"];
  2 -->|output| 3;
  189572e7-e0e6-4818-91b1-441beced67a4["Output\noutput"];
  3 --> 189572e7-e0e6-4818-91b1-441beced67a4;
  style 189572e7-e0e6-4818-91b1-441beced67a4 stroke:#2c3143,stroke-width:4px;
	

flowchart TD
  0["ℹ️ Input Dataset\ninput image"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nfilter rules"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Filter 2-D image"];
  0 -->|output| 2;
  3["Threshold image"];
  2 -->|output| 3;
  4["Convert binary image to label map"];
  3 -->|output| 4;
  5["Extract image features"];
  4 -->|output| 5;
  6["Filter label map by rules"];
  5 -->|output| 6;
  4 -->|output| 6;
  1 -->|output| 6;
  f6f7f638-0f3c-404e-ab2e-5281a0393060["Output\noutput"];
  6 --> f6f7f638-0f3c-404e-ab2e-5281a0393060;
  style f6f7f638-0f3c-404e-ab2e-5281a0393060 stroke:#2c3143,stroke-width:4px;
  7["Extract image features"];
  6 -->|output| 7;
  0 -->|output| 7;
  31da5e27-19fe-465e-95f0-96d3f6dcaba4["Output\noutput"];
  7 --> 31da5e27-19fe-465e-95f0-96d3f6dcaba4;
  style 31da5e27-19fe-465e-95f0-96d3f6dcaba4 stroke:#2c3143,stroke-width:4px;
	

Importing into Galaxy

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: