mRNA-Seq BY-COVID Pipeline: Counts

transcriptomics-minerva-pathways/galaxy-workflow-mrna-seq-by-covid-pipeline--counts

Author(s)
Iacopo Cristoferi, Helena Rasche, Clinical Bioinformatics Unit, Pathology Department, Eramus Medical Center
Version
1
Last updated
Mar 28, 2024
License
GPL-3.0-or-later
Tags
name:BY-COVID

Features
Tutorial
Pathway analysis with the MINERVA Platform
Other workflows associated with this material
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00241
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\nmRNA-Seq Reads"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nUCSC Genome"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["FastQC"];
  0 -->|output| 2;
  3["Cutadapt"];
  0 -->|output| 3;
  4["FastQC"];
  3 -->|out1| 4;
  5["HISAT2"];
  3 -->|out1| 5;
  6["featureCounts"];
  5 -->|output_alignments| 6;
  5cb5bd5d-df81-4463-8002-e89551780f01["Output\noutput_feature_lengths"];
  6 --> 5cb5bd5d-df81-4463-8002-e89551780f01;
  style 5cb5bd5d-df81-4463-8002-e89551780f01 stroke:#2c3143,stroke-width:4px;
  5dec13e1-0011-472c-a72d-6715fe55c23c["Output\noutput_short"];
  6 --> 5dec13e1-0011-472c-a72d-6715fe55c23c;
  style 5dec13e1-0011-472c-a72d-6715fe55c23c stroke:#2c3143,stroke-width:4px;
  7["Read Distribution"];
  5 -->|output_alignments| 7;
  1 -->|output| 7;
  8["Gene Body Coverage BAM"];
  5 -->|output_alignments| 8;
  1 -->|output| 8;
  9["Multi QC raw reads"];
  2 -->|text_file| 9;
  4 -->|text_file| 9;
  3 -->|report| 9;
  5 -->|summary_file| 9;
  7 -->|output| 9;
  8 -->|outputtxt| 9;
  6 -->|output_summary| 9;
  9217af4e-e34c-4a49-9d67-4b3df511ac2c["Output\nhtml_report"];
  9 --> 9217af4e-e34c-4a49-9d67-4b3df511ac2c;
  style 9217af4e-e34c-4a49-9d67-4b3df511ac2c stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset collection mRNA-Seq Reads
Input dataset UCSC Genome

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy1 featureCounts
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1 MultiQC Multi QC raw reads

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/featurecounts/featurecounts/2.0.3+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.4+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/5.0.1+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/5.0.1+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
1 0836149a2 2023-12-19 11:46:27 cleanups

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/minerva-pathways/workflows/Galaxy-Workflow-mRNA-Seq_BY-COVID_Pipeline__Counts.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