Workflows

These workflows are associated with Creating a new tutorial

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\nSRR891268_R1_20M.fastq.gz"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nSRR891268_R2_20M.fastq.gz"];
  style 1 stroke:#2c3143,stroke-width:4px;
  10["Unique"];
  9 -->|out_file1| 10;
  11["Text transformation"];
  10 -->|outfile| 11;
  12["Concatenate datasets"];
  6 -->|out_file1| 12;
  11 -->|output| 12;
  13["Unique"];
  12 -->|out_file1| 13;
  14["seqtk_subseq"];
  0 -->|output| 14;
  13 -->|outfile| 14;
  15["Text transformation"];
  13 -->|outfile| 15;
  16["seqtk_subseq"];
  1 -->|output| 16;
  15 -->|output| 16;
  2["FASTQ to Tabular"];
  0 -->|output| 2;
  3["Cutadapt"];
  0 -->|output| 3;
  1 -->|output| 3;
  4["Cut"];
  2 -->|output_file| 4;
  5["Bowtie2"];
  3 -->|out1| 5;
  3 -->|out2| 5;
  6["Select random lines"];
  4 -->|output| 6;
  7["BAM-to-SAM"];
  5 -->|output| 7;
  8["Filter"];
  7 -->|output1| 8;
  9["Cut"];
  8 -->|out_file1| 9;
	

flowchart TD
  0["ℹ️ Input Dataset\nAPI Request file"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Copernicus Climate Data Store"];
  0 -->|output| 1;
	

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: