QC report

transcriptomics-rna-seq-reads-to-counts/qc-report

Author(s)

Version
2
Last updated
Nov 15, 2020
License
None Specified, defaults to CC-BY-4.0
Tags
transcriptomics

Features
Tutorial
1: RNA-Seq reads to counts
Other workflows associated with this material
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00250
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\nReference genes"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Collection\nBAM files"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Infer Experiment"];
  1 -->|output| 2;
  0 -->|output| 2;
  3["MarkDuplicates"];
  1 -->|output| 3;
  4["Samtools idxstats"];
  1 -->|output| 4;
  5["MultiQC"];
  2 -->|output| 5;
  3 -->|metrics_file| 5;
  4 -->|output| 5;

Inputs

Input Label
Input dataset Reference genes
Input dataset collection BAM files

Outputs

From Output Label
Input dataset Reference genes
Input dataset collection BAM files
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7 MultiQC

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7 View in ToolShed
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1 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
4 e30984605 2020-11-15 11:14:55 Update qc workflow
3 bf6f08b6a 2020-11-14 05:37:17 Fix tags attribute
2 d42f753af 2020-11-14 01:15:21 Fix workflow for failing travis test
1 cea2aaab2 2020-11-12 10:21:35 Reconfiguration of some content

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-reads-to-counts/workflows/qc_report.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