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

Download Galaxy Workflow.ga EU US AU Import to another server (≥23.0+ only!) 
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 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: