Exome Seq Training Full W Cached Ref

variant-analysis-exome-seq/workflow-exome-seq-full

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:W00261
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nfather_R1"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nfather_R2"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nmother_R1"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nmother_R2"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nproband_R1"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["ℹ️ Input Dataset\nproband_R2"];
  style 5 stroke:#2c3143,stroke-width:4px;
  6["ℹ️ Input Dataset\nPEDigree data"];
  style 6 stroke:#2c3143,stroke-width:4px;
  7["FastQC"];
  0 -->|output| 7;
  8["FastQC"];
  1 -->|output| 8;
  9["Map with BWA-MEM"];
  0 -->|output| 9;
  1 -->|output| 9;
  10["FastQC"];
  2 -->|output| 10;
  11["FastQC"];
  3 -->|output| 11;
  12["Map with BWA-MEM"];
  2 -->|output| 12;
  3 -->|output| 12;
  13["FastQC"];
  4 -->|output| 13;
  14["FastQC"];
  5 -->|output| 14;
  15["Map with BWA-MEM"];
  4 -->|output| 15;
  5 -->|output| 15;
  16["Samtools view"];
  9 -->|bam_output| 16;
  17["Samtools view"];
  12 -->|bam_output| 17;
  18["MultiQC"];
  7 -->|text_file| 18;
  8 -->|text_file| 18;
  10 -->|text_file| 18;
  11 -->|text_file| 18;
  13 -->|text_file| 18;
  14 -->|text_file| 18;
  de867748-890a-454c-baf3-6a9313269975["Output\nmultiqc_input_data"];
  18 --> de867748-890a-454c-baf3-6a9313269975;
  style de867748-890a-454c-baf3-6a9313269975 stroke:#2c3143,stroke-width:4px;
  19["Samtools view"];
  15 -->|bam_output| 19;
  20["RmDup"];
  16 -->|outputsam| 20;
  21["RmDup"];
  17 -->|outputsam| 21;
  22["RmDup"];
  19 -->|outputsam| 22;
  23["FreeBayes"];
  20 -->|output1| 23;
  21 -->|output1| 23;
  22 -->|output1| 23;
  24["bcftools norm"];
  23 -->|output_vcf| 24;
  25["SnpEff eff:"];
  24 -->|output_file| 25;
  4aab5884-4099-4e41-a82d-c4e1ff19609f["Output\nsnpeff_variant_stats"];
  25 --> 4aab5884-4099-4e41-a82d-c4e1ff19609f;
  style 4aab5884-4099-4e41-a82d-c4e1ff19609f stroke:#2c3143,stroke-width:4px;
  e5a2fbc7-acdd-4782-822a-91568cb8d5b8["Output\nnormalized_snpeff_annotated_variants"];
  25 --> e5a2fbc7-acdd-4782-822a-91568cb8d5b8;
  style e5a2fbc7-acdd-4782-822a-91568cb8d5b8 stroke:#2c3143,stroke-width:4px;
  26["GEMINI load"];
  25 -->|snpeff_output| 26;
  6 -->|output| 26;
  27["GEMINI inheritance pattern"];
  26 -->|outfile| 27;
  07bd4bba-e7d9-48a8-b812-5dc2b07712bd["Output\ncandidate_mutations"];
  27 --> 07bd4bba-e7d9-48a8-b812-5dc2b07712bd;
  style 07bd4bba-e7d9-48a8-b812-5dc2b07712bd stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset father_R1
Input dataset father_R2
Input dataset mother_R1
Input dataset mother_R2
Input dataset proband_R1
Input dataset proband_R2
Input dataset PEDigree data

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1 MultiQC
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/bwa/bwa_mem/0.7.17.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0 View in ToolShed
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/multiqc/multiqc/1.11+galaxy1 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_full.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