mRNA-Seq BY-COVID Pipeline: Counts
transcriptomics-minerva-pathways/galaxy-workflow-mrna-seq-by-covid-pipeline--counts
Launch in Tutorial Mode
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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;
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 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
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