GTN - Sequence Analyses - Quality Control (imported from uploaded file)

sequence-analysis-quality-control/quality-control

Author(s)

Version
5
Last updated
Apr 21, 2021
License
None Specified, defaults to CC-BY-4.0
Tags
sequence-analysis

Features
Tutorial
Quality Control
Workflow Testing
Tests: ✅
Results:
FAIRness PURL
https://gxy.io/GTN:W00184
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\nreads_2"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nreads_1"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["FastQC"];
  0 -->|output| 2;
  1f4fad7b-11e7-4ec5-b73d-835080c47e70["Output\nreads_2_fastqc"];
  2 --> 1f4fad7b-11e7-4ec5-b73d-835080c47e70;
  style 1f4fad7b-11e7-4ec5-b73d-835080c47e70 stroke:#2c3143,stroke-width:4px;
  3["Cutadapt"];
  1 -->|output| 3;
  12a1bc96-cfdd-4ed8-b062-433833e09aee["Output\nreads_1_cutadapt"];
  3 --> 12a1bc96-cfdd-4ed8-b062-433833e09aee;
  style 12a1bc96-cfdd-4ed8-b062-433833e09aee stroke:#2c3143,stroke-width:4px;
  4["FastQC"];
  1 -->|output| 4;
  12e19f0b-102a-4470-9bc8-e362bb4e2c91["Output\nreads_1_fastqc"];
  4 --> 12e19f0b-102a-4470-9bc8-e362bb4e2c91;
  style 12e19f0b-102a-4470-9bc8-e362bb4e2c91 stroke:#2c3143,stroke-width:4px;
  5["Cutadapt"];
  1 -->|output| 5;
  0 -->|output| 5;
  b7c138cc-10d0-4bd0-b960-a3b5e60f29cd["Output\nreads_cutadapt"];
  5 --> b7c138cc-10d0-4bd0-b960-a3b5e60f29cd;
  style b7c138cc-10d0-4bd0-b960-a3b5e60f29cd stroke:#2c3143,stroke-width:4px;
  6["MultiQC"];
  4 -->|text_file| 6;
  2 -->|text_file| 6;
  fa7f541d-b9be-4283-afa1-8398d89f345e["Output\nmultiqc"];
  6 --> fa7f541d-b9be-4283-afa1-8398d89f345e;
  style fa7f541d-b9be-4283-afa1-8398d89f345e stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset reads_2
Input dataset reads_1

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1 FastQC
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.3 Cutadapt
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1 FastQC
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.3 Cutadapt
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1 MultiQC

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.3 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
6 505f7550f 2021-04-20 17:22:17 update-workflows
5 667ff3de9 2020-01-22 10:59:29 annotation
4 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
3 7b4cb6d1d 2018-09-24 15:59:49 Replace Trim Galore with Cutadapt
2 2204ebb5e 2018-09-13 12:57:10 Expand the QC tutorial and add workflow testing
1 3048a0c69 2017-06-27 17:19:20 workflows

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/workflows/quality_control.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