mRNA-Seq BY-COVID Pipeline: Analysis

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

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:W00240
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\nfeatureCounts: Counts"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nfactordata"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Collection\nfeatureCounts: Lengths"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Column join"];
  0 -->|output| 3;
  4["Extract dataset"];
  2 -->|output| 4;
  5["countdata"];
  3 -->|tabular_output| 5;
  e8dcfaaf-0d8d-46eb-8cc9-ce2fbdfc45e5["Output\ncount_data"];
  5 --> e8dcfaaf-0d8d-46eb-8cc9-ce2fbdfc45e5;
  style e8dcfaaf-0d8d-46eb-8cc9-ce2fbdfc45e5 stroke:#2c3143,stroke-width:4px;
  6["annodata"];
  3 -->|tabular_output| 6;
  7["Replace Text"];
  5 -->|outfile| 7;
  8["limma DEG analysis"];
  6 -->|out_tab| 8;
  7 -->|outfile| 8;
  1 -->|output| 8;
  1c8d7950-1003-4c86-9986-c6ed1264cd8b["Output\nlimma_report"];
  8 --> 1c8d7950-1003-4c86-9986-c6ed1264cd8b;
  style 1c8d7950-1003-4c86-9986-c6ed1264cd8b stroke:#2c3143,stroke-width:4px;
  9["Extract dataset"];
  8 -->|outTables| 9;
  10["MINERVA Formatting"];
  9 -->|output| 10;
  9ce4f48b-e742-4b7c-9bde-5d51f11068d3["Output\nminerva_table"];
  10 --> 9ce4f48b-e742-4b7c-9bde-5d51f11068d3;
  style 9ce4f48b-e742-4b7c-9bde-5d51f11068d3 stroke:#2c3143,stroke-width:4px;
  11["Join two Datasets"];
  9 -->|output| 11;
  4 -->|output| 11;
  12["Compute"];
  11 -->|out_file1| 12;
  13["Cut"];
  12 -->|out_file1| 13;
  14["Unique"];
  13 -->|out_file1| 14;
  15["Cut"];
  14 -->|outfile| 15;
  16["Cut"];
  14 -->|outfile| 16;
  17["goseq"];
  15 -->|out_file1| 17;
  16 -->|out_file1| 17;

Inputs

Input Label
Input dataset collection featureCounts: Counts
Input dataset factordata
Input dataset collection featureCounts: Lengths

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1 Sort countdata
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0 limma limma DEG analysis
Cut1 Cut MINERVA Formatting

Tools

Tool Links
Cut1
__EXTRACT_DATASET__
join1
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.16.0+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.50.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0 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
  1. Click on Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
  2. Click on Import at the top-right of the screen
  3. 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”
  4. 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__Analysis.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