Workflows

These workflows are associated with Mapping

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 Dataset\nreads_1"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nreads_2"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["FastQC"];
  0 -->|output| 2;
  3["FastQC"];
  1 -->|output| 3;
  4["Trim Galore!"];
  0 -->|output| 4;
  1 -->|output| 4;
  5["MultiQC"];
  3 -->|text_file| 5;
  2 -->|text_file| 5;
  6["Bowtie2"];
  4 -->|trimmed_reads_pair1| 6;
  4 -->|trimmed_reads_pair2| 6;
  cb22563a-fece-4b63-9d85-ff5817edb5c3["Output\nbowtie2_mapping_stats"];
  6 --> cb22563a-fece-4b63-9d85-ff5817edb5c3;
  style cb22563a-fece-4b63-9d85-ff5817edb5c3 stroke:#2c3143,stroke-width:4px;
  7["Samtools stats"];
  6 -->|output| 7;
  490620d4-f083-4999-bb33-73a2a1f736b4["Output\nbam_stats_1"];
  7 --> 490620d4-f083-4999-bb33-73a2a1f736b4;
  style 490620d4-f083-4999-bb33-73a2a1f736b4 stroke:#2c3143,stroke-width:4px;
  8["JBrowse"];
  6 -->|output| 8;
	

flowchart TD
  0["ℹ️ Input Dataset\nreads_1"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nreads_2"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["FastQC"];
  0 -->|output| 2;
  3["FastQC"];
  1 -->|output| 3;
  4["Trim Galore!"];
  0 -->|output| 4;
  1 -->|output| 4;
  5["MultiQC"];
  3 -->|text_file| 5;
  2 -->|text_file| 5;
  6["Bowtie2"];
  4 -->|trimmed_reads_pair1| 6;
  4 -->|trimmed_reads_pair2| 6;
  d2674912-28a6-45f3-ac48-6635eabe47b7["Output\nbowtie2_mapping_stats"];
  6 --> d2674912-28a6-45f3-ac48-6635eabe47b7;
  style d2674912-28a6-45f3-ac48-6635eabe47b7 stroke:#2c3143,stroke-width:4px;
  7["Stats"];
  6 -->|output| 7;
  96de3c0c-4d7e-423b-8e9b-9a12a011d726["Output\nbam_stats_1"];
  7 --> 96de3c0c-4d7e-423b-8e9b-9a12a011d726;
  style 96de3c0c-4d7e-423b-8e9b-9a12a011d726 stroke:#2c3143,stroke-width:4px;
  8["Filter"];
  6 -->|output| 8;
  9["Stats"];
  8 -->|out_file1| 9;
  9603a94a-dcd8-4c1f-89cd-bb31d8572783["Output\nbam_stats_2"];
  9 --> 9603a94a-dcd8-4c1f-89cd-bb31d8572783;
  style 9603a94a-dcd8-4c1f-89cd-bb31d8572783 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: