Workflows
These workflows are associated with From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis
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.
Simple COVID-19 - PE Variation
Last updated Jun 24, 2020
Launch in Tutorial Mode
License:
None Specified, defaults to
CC-BY-4.0
Tests: ❌
Results: Not yet automated
flowchart TD 0["Input dataset"]; 1["Input dataset"]; 2["Faster Download and Extract Reads in FASTQ"]; 3["fastp"]; 4["Map with BWA-MEM"]; 5["MarkDuplicates"]; 6["Realign reads"]; 7["Samtools stats"]; 8["Insert indel qualities"]; 9["Call variants"]; 10["SnpEff eff:"]; 11["SnpSift Extract Fields"]; 12["MultiQC"]; 1 -->|output| 2; 2 -->|list_paired| 3; 3 -->|output_paired_coll| 4; 0 -->|output| 4; 4 -->|bam_output| 5; 5 -->|outFile| 6; 0 -->|output| 6; 5 -->|outFile| 7; 6 -->|realigned| 8; 0 -->|output| 8; 8 -->|output| 9; 0 -->|output| 9; 9 -->|variants| 10; 10 -->|snpeff_output| 11; 3 -->|report_json| 12; 7 -->|output| 12; 5 -->|metrics_file| 12; 10 -->|csvFile| 12;
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: