Workflow Methylation Seq

epigenetics-methylation-seq/methylation-seq

Author(s)

version Version
3
last_modification Last updated
Jan 23, 2020
license License
None Specified, defaults to CC-BY-4.0
galaxy-tags Tags
epigenetics

Features

Tutorial
hands_on DNA Methylation data analysis

Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00070
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode question
galaxy-download Download
flowchart TD
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  1["ℹ️ Input Dataset\nInput dataset"];
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  2["ℹ️ Input Dataset\nInput dataset"];
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  3["ℹ️ Input Dataset\nInput dataset"];
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  4["ℹ️ Input Dataset\nInput dataset"];
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  5["ℹ️ Input Dataset\nInput dataset"];
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  6["ℹ️ Input Dataset\nInput dataset"];
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  8["ℹ️ Input Dataset\nInput dataset"];
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  9["FastQC"];
  0 -->|output| 9;
  10["FastQC"];
  1 -->|output| 10;
  11["bwameth"];
  0 -->|output| 11;
  1 -->|output| 11;
  12["Replace column"];
  3 -->|output| 12;
  4 -->|output| 12;
  13["metilene"];
  2 -->|output| 13;
  5 -->|output| 13;
  3 -->|output| 13;
  8 -->|output| 13;
  7 -->|output| 13;
  6 -->|output| 13;
  14["MethylDackel"];
  11 -->|output| 14;
  15["MethylDackel"];
  11 -->|output| 15;
  16["Select last"];
  12 -->|outfile_replace| 16;
  17["Select last"];
  15 -->|outFileExtractCpGFraction| 17;
  18["computeMatrix"];
  16 -->|outfile| 18;
  2 -->|output| 18;
  19["Text reformatting"];
  17 -->|outfile| 19;
  20["computeMatrix"];
  19 -->|outfile| 20;
  2 -->|output| 20;
  21["plotProfile"];
  20 -->|outFileName| 21;
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Inputs

Input Label
Input dataset
Input dataset
Input dataset
Input dataset
Input dataset
Input dataset
Input dataset
Input dataset
Input dataset

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/2.5.1.1.0 plotProfile

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/2.5.1.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/2.5.1.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/pileometh/pileometh/0.3.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.68 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.0.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/rnateam/metilene/metilene/0.2.6.1

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

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
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:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
4 667ff3de9 2020-01-22 10:59:29 annotation
3 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
2 b97e27513 2018-05-22 15:36:31 add methylation workflow test data
1 b169a31b9 2018-05-22 15:35:26 add methylation workflow test data

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/methylation-seq/workflows/methylation-seq.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