Mapping And Molecular Identification Of Phenotype Causing Mutations

variant-analysis-mapping-by-sequencing/workflow-arabidopsis

Author(s)

Version
3
Last updated
Oct 18, 2022
License
None Specified, defaults to CC-BY-4.0
Tags
variant-analysis

Features
Tutorial
Mapping and molecular identification of phenotype-causing mutations
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00262
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\nA. thaliana TAIR10 ref genome"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\naligned reads from outcrossed F2 pool"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\naligned reads from Ler mapping strain"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["SnpEff Download"];
  4["Replace parts of text"];
  0 -->|output| 4;
  5["MiModD Variant Calling"];
  4 -->|outfile| 5;
  2 -->|output| 5;
  1 -->|output| 5;
  6["MiModD Extract Variant Sites"];
  5 -->|ofile| 6;
  7["MiModD NacreousMap"];
  6 -->|output_vcf| 7;
  8["MiModD VCF Filter"];
  6 -->|output_vcf| 8;
  9["SnpEff"];
  8 -->|outputfile| 9;
  3 -->|snpeff_db| 9;
  10["MiModD Report Variants"];
  9 -->|snpeff_output| 10;

Inputs

Input Label
Input dataset A. thaliana TAIR10 ref genome
Input dataset aligned reads from outcrossed F2 pool
Input dataset aligned reads from Ler mapping strain

Outputs

From Output Label

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_map/0.1.8_1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varcall/0.1.8_1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varextract/0.1.8_1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varreport/0.1.8_1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_vcf_filter/0.1.8_1 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
3 3f568e83c 2022-10-06 18:21:23 Correct some ancient URLs
2 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
1 a14e0a4b7 2018-03-12 16:07:18 mapping-by-sequencing tutorial: add workflow

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/mapping-by-sequencing/workflows/workflow-arabidopsis.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