CUT&RUN

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Collection\nInput Dataset Collection"];
  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\nI certify that I am not using this workflow for commercial purposes"];
  style 2 fill:#ded,stroke:#393,stroke-width:4px;
  3["Trim Galore!"];
  0 -->|output| 3;
  4["Flatten collection"];
  0 -->|output| 4;
  5["Bowtie2"];
  3 -->|trimmed_reads_paired_collection| 5;
  6["Falco"];
  4 -->|output| 6;
  7["plotFingerprint"];
  5 -->|output| 7;
  8["Filter BAM"];
  5 -->|output| 8;
  9["MultiQC"];
  6 -->|text_file| 9;
  10["MarkDuplicates"];
  8 -->|out_file1| 10;
  11["Select"];
  10 -->|metrics_file| 11;
  12["Falco"];
  10 -->|outFile| 12;
  13["bedtools BAM to BED"];
  10 -->|outFile| 13;
  14["Paired-end histogram"];
  10 -->|outFile| 14;
  15["Transpose"];
  11 -->|out_file1| 15;
  16["MultiQC"];
  12 -->|text_file| 16;
  17["MACS2 callpeak"];
  13 -->|output| 17;
  18["Extract dataset"];
  17 -->|output_narrowpeaks| 18;
  19["Extract dataset"];
  17 -->|output_narrowpeaks| 19;
  20["Wig/BedGraph-to-bigWig"];
  17 -->|output_treat_pileup| 20;
  21["bedtools Intersect intervals"];
  18 -->|output| 21;
  19 -->|output| 21;
  22["bedtools Intersect intervals"];
  21 -->|output| 22;
  1 -->|output| 22;
  23["Extract Genomic DNA"];
  22 -->|output| 23;
  24["Cut"];
  22 -->|output| 24;
  25["MEME-ChIP"];
  23 -->|output| 25;
  2 -->|output| 25;
  866ccdf7-bdb9-471d-b68d-4ef3a557ee71["Output\nMEME-ChIP html output"];
  25 --> 866ccdf7-bdb9-471d-b68d-4ef3a557ee71;
  style 866ccdf7-bdb9-471d-b68d-4ef3a557ee71 stroke:#2c3143,stroke-width:4px;
  26["computeMatrix"];
  20 -->|out_file1| 26;
  24 -->|out_file1| 26;
  27["plotHeatmap"];
  26 -->|outFileName| 27;
  75ea7005-fe2d-4aac-b587-60281adc6ca3["Output\nheatmap"];
  27 --> 75ea7005-fe2d-4aac-b587-60281adc6ca3;
  style 75ea7005-fe2d-4aac-b587-60281adc6ca3 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

1. Click on galaxy-workflows-activity Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
2. Click on galaxy-upload Import at the top-right of the screen
3. 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”
4. 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