Exome Seq Training Pre-Mapped W Cached Ref

variant-analysis-exome-seq/workflow-exome-seq-from-premapped

Author(s)
Wolfgang Maier
Version
5
Last updated
Jul 19, 2023
License
MIT
Tags
variant-analysis

Features
Tutorial
Exome sequencing data analysis for diagnosing a genetic disease
Other workflows associated with this material
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00260
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nFather data"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nMother data"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nProband data"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nPEDigree data"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["Samtools view"];
  0 -->|output| 4;
  5["Samtools view"];
  1 -->|output| 5;
  6["Samtools view"];
  2 -->|output| 6;
  7["RmDup"];
  4 -->|outputsam| 7;
  8["RmDup"];
  5 -->|outputsam| 8;
  9["RmDup"];
  6 -->|outputsam| 9;
  10["FreeBayes"];
  7 -->|output1| 10;
  8 -->|output1| 10;
  9 -->|output1| 10;
  11["bcftools norm"];
  10 -->|output_vcf| 11;
  12["SnpEff eff:"];
  11 -->|output_file| 12;
  974b6b15-ccf7-4fe8-8a71-2b3fe8b45272["Output\nsnpeff_variant_stats"];
  12 --> 974b6b15-ccf7-4fe8-8a71-2b3fe8b45272;
  style 974b6b15-ccf7-4fe8-8a71-2b3fe8b45272 stroke:#2c3143,stroke-width:4px;
  083b9686-5c6d-495f-9257-7243896e64d7["Output\nnormalized_snpeff_annotated_variants"];
  12 --> 083b9686-5c6d-495f-9257-7243896e64d7;
  style 083b9686-5c6d-495f-9257-7243896e64d7 stroke:#2c3143,stroke-width:4px;
  13["GEMINI load"];
  12 -->|snpeff_output| 13;
  3 -->|output| 13;
  14["GEMINI inheritance pattern"];
  13 -->|outfile| 14;
  c5a64822-3c68-495e-b2fd-4642b1aabb5a["Output\ncandidate_mutations"];
  14 --> c5a64822-3c68-495e-b2fd-4642b1aabb5a;
  style c5a64822-3c68-495e-b2fd-4642b1aabb5a stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset Father data
Input dataset Mother data
Input dataset Proband data
Input dataset PEDigree data

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2 SnpEff eff:
toolshed.g2.bx.psu.edu/repos/iuc/gemini_inheritance/gemini_inheritance/0.20.1 GEMINI inheritance pattern

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.6+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.15.1+galaxy3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/gemini_inheritance/gemini_inheritance/0.20.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2 View in ToolShed

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 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
5 75e124804 2023-07-17 15:46:12 Update exome-seq tutorial/WFs to latest tool versions
4 667ff3de9 2020-01-22 10:59:29 annotation
3 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
2 07bdd3bee 2019-09-21 07:45:07 Update variant analysis tutorials
1 a2aa175b0 2019-06-14 16:59:08 Reworked exome-seq tutorial

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/exome-seq/workflows/workflow_exome_seq_from_premapped.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