CUT&RUN GTN

Run Workflow in Galaxy

• Galaxy Main
• Galaxy France
• Galaxy Europe
• Galaxy Australia
• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Collection\nFastq PE inputs"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nGATA1_ChIP-Seq peaks"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Parameter\nNon-Commercial purposes"];
  style 2 fill:#ded,stroke:#393,stroke-width:4px;
  3["Flatten collection for FastQC"];
  0 -->|output| 3;
  4["Trim Galore!"];
  0 -->|output| 4;
  5["FastQC on raw reads"];
  3 -->|output| 5;
  6["Bowtie2"];
  4 -->|trimmed_reads_paired_collection| 6;
  7["MultiQC"];
  5 -->|text_file| 7;
  8["Filter BAM"];
  6 -->|output| 8;
  9["MarkDuplicates"];
  8 -->|out_file1| 9;
  10["FastQC"];
  9 -->|outFile| 10;
  11["Paired-end histogram"];
  9 -->|outFile| 11;
  12["bedtools BAM to BED"];
  9 -->|outFile| 12;
  13["MACS2 callpeak"];
  12 -->|output| 13;
  14["Get Rep1 peaks"];
  13 -->|output_narrowpeaks| 14;
  15["Get Rep2 peaks"];
  13 -->|output_narrowpeaks| 15;
  16["Get Robust GATA1 CUT and RUN peaks"];
  14 -->|output| 16;
  15 -->|output| 16;
  17["Get True GATA1 CUT and RUN peaks"];
  16 -->|output| 17;
  1 -->|output| 17;
  18["Extract Genomic DNA"];
  17 -->|output| 18;
  19["Get motif"];
  18 -->|output| 19;
  2 -->|output| 19;
  af32c4fc-332a-4a6b-af0e-fd11d31a5bb5["Output\nMEME-ChIP html output"];
  19 --> af32c4fc-332a-4a6b-af0e-fd11d31a5bb5;
  style af32c4fc-332a-4a6b-af0e-fd11d31a5bb5 stroke:#2c3143,stroke-width:4px;

Inputs

Outputs

Tools

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.

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:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/cut_and_run/workflows/main_workflow.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows