Workflows
These workflows are associated with 1: RNA-Seq reads to counts
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.
QC report
Last updated Nov 15, 2020
Launch in Tutorial Mode
License:
None Specified, defaults to
CC-BY-4.0
Tests: ❌
Results: Not yet automated
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;
RNA Seq Reads To Counts
Last updated Jan 23, 2020
Launch in Tutorial Mode
License:
None Specified, defaults to
CC-BY-4.0
Tests: ❌
Results: Not yet automated
flowchart TD 0["ℹ️ Input Collection\nInput FASTQs collection"]; style 0 stroke:#2c3143,stroke-width:4px; 1["ℹ️ Input Dataset\nInput Reference gene BED"]; style 1 stroke:#2c3143,stroke-width:4px; 10["Infer Experiment"]; 5 -->|output_alignments| 10; 1 -->|output| 10; 11["Read Distribution"]; 5 -->|output_alignments| 11; 1 -->|output| 11; 12["Column Join"]; 6 -->|output_short| 12; 13["MultiQC"]; 4 -->|text_file| 13; 3 -->|report| 13; 10 -->|output| 13; 7 -->|metrics_file| 13; 8 -->|output| 13; 9 -->|outputtxt| 13; 11 -->|output| 13; 6 -->|output_summary| 13; 5 -->|summary_file| 13; 2["FastQC raw reads"]; 0 -->|output| 2; 3["Cutadapt"]; 0 -->|output| 3; 4["FastQC post QC"]; 3 -->|out1| 4; 5["HISAT2"]; 3 -->|out1| 5; 6["featureCounts"]; 5 -->|output_alignments| 6; 7["MarkDuplicates"]; 5 -->|output_alignments| 7; 8["Samtools idxstats"]; 5 -->|output_alignments| 8; 9["Gene Body Coverage BAM"]; 5 -->|output_alignments| 9; 1 -->|output| 9;
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 galaxy-upload 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