Mitogenome-Assembly-VGP0

assembly-mitochondrion-assembly/main-workflow

Author(s)
VGP, Galaxy
Version
1
Last updated
Sep 3, 2024
License
CC-BY-4.0
Tags
Reviewed
VGP

Features
Tutorial
Assembly of the mitochondrial genome from PacBio HiFi reads
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00285
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 Collection\nCollection of Pacbio Data"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Parameter\nSpecies name latin name"];
  style 1 fill:#ded,stroke:#393,stroke-width:4px;
  2["ℹ️ Input Parameter\nEmail adress"];
  style 2 fill:#ded,stroke:#393,stroke-width:4px;
  3["MitoHiFi"];
  2 -->|output| 3;
  1 -->|output| 3;
  4["MitoHiFi"];
  0 -->|output| 4;
  3 -->|fasta_reference| 4;
  3 -->|genbank_reference| 4;
  31807e4b-e616-4742-92e0-934e6c3c09ae["Output\ncontigs_stats"];
  4 --> 31807e4b-e616-4742-92e0-934e6c3c09ae;
  style 31807e4b-e616-4742-92e0-934e6c3c09ae stroke:#2c3143,stroke-width:4px;
  8393c665-a328-4698-93e5-198c6fea52dd["Output\nmitogenome_coverage"];
  4 --> 8393c665-a328-4698-93e5-198c6fea52dd;
  style 8393c665-a328-4698-93e5-198c6fea52dd stroke:#2c3143,stroke-width:4px;
  85061673-df5e-480d-920a-a11c72bf8f56["Output\nmitogenome_annotation"];
  4 --> 85061673-df5e-480d-920a-a11c72bf8f56;
  style 85061673-df5e-480d-920a-a11c72bf8f56 stroke:#2c3143,stroke-width:4px;
  fe4d1d3d-9caa-45f6-944e-c4b101105dd1["Output\nmitogenome_genbank"];
  4 --> fe4d1d3d-9caa-45f6-944e-c4b101105dd1;
  style fe4d1d3d-9caa-45f6-944e-c4b101105dd1 stroke:#2c3143,stroke-width:4px;
  5["Compress files"];
  4 -->|mitogenome_fasta| 5;
  6f918a08-1ca1-4d6e-a4d8-7e65e13a65ed["Output\noutput_file"];
  5 --> 6f918a08-1ca1-4d6e-a4d8-7e65e13a65ed;
  style 6f918a08-1ca1-4d6e-a4d8-7e65e13a65ed stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset collection Collection of Pacbio Data
Input parameter Species name (latin name)
Input parameter Email adress

Outputs

From Output Label
Input parameter Species name (latin name)
Input parameter Email adress
toolshed.g2.bx.psu.edu/repos/bgruening/mitohifi/mitohifi/3+galaxy0 MitoHiFi
toolshed.g2.bx.psu.edu/repos/iuc/compress_file/compress_file/0.1.0 Compress file(s)

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/bgruening/mitohifi/mitohifi/3+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/compress_file/compress_file/0.1.0 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
2 d6520a5b9 2024-09-02 21:00:48 workflow reformating
1 7e2bcd1f0 2024-08-19 14:51:36 Creation of the tutorial skeleton

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/assembly/tutorials/mitochondrion-assembly/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