Data QC - upgraded

assembly-largegenome/galaxy-workflow-data-qc

Author(s)
Anna Syme
Version
2
Last updated
May 8, 2024
License
GPL-3.0-or-later
Tags
LG-WF
GTN

Features
Tutorial
Large genome assembly and polishing
Other workflows associated with this material
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00013
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\nInput file: long reads"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nInput file: Illumina reads R1"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nInput file: Illumina reads R2"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Nanoplot: long reads"];
  0 -->|output| 3;
  73d0e4cf-366e-41c1-810a-b269638826b3["Output\nNanoPlot on input dataset(s): HTML report"];
  3 --> 73d0e4cf-366e-41c1-810a-b269638826b3;
  style 73d0e4cf-366e-41c1-810a-b269638826b3 stroke:#2c3143,stroke-width:4px;
  4["FastQC on R1"];
  1 -->|output| 4;
  5["FastQC on R2"];
  2 -->|output| 5;
  6["MultiQC: combine fastQC reports"];
  4 -->|text_file| 6;
  5 -->|text_file| 6;
  8baf8700-876e-4a74-ad99-6e656f3ba618["Output\nMultiQC on input dataset(s): Webpage"];
  6 --> 8baf8700-876e-4a74-ad99-6e656f3ba618;
  style 8baf8700-876e-4a74-ad99-6e656f3ba618 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset Input file: long reads
Input dataset Input file: Illumina reads R1
Input dataset Input file: Illumina reads R2

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.42.0+galaxy1 NanoPlot Nanoplot: long reads
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1 MultiQC MultiQC: combine fastQC reports

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0 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/nanoplot/nanoplot/1.42.0+galaxy1 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 d35221f65 2024-05-07 09:33:04 Update Galaxy-Workflow-Data_QC.ga
4 a737e5f1b 2024-05-01 04:19:51 Rename Galaxy-Workflow-Data_QC_-_upgraded.ga to Galaxy-Workflow-Data_QC.ga
3 9ca497557 2024-05-01 04:18:38 Rename Galaxy-Workflow-Data_QC.ga to Galaxy-Workflow-Data_QC_old.ga
2 62e77944b 2023-02-17 09:53:23 add/complete creator info on workflows
1 9fcb3aeec 2022-10-07 06:24:16 large genome tutorial

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Data_QC.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