Simple COVID-19 - PE Variation

Run Workflow in Galaxy

• Galaxy Main
• Galaxy Australia
• Galaxy Europe
• Galaxy France
• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Dataset\nNC_045512.2 fasta file"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nSRA Manifest"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Faster Download and Extract Reads in FASTQ"];
  1 -->|output| 2;
  3["fastp"];
  2 -->|list_paired| 3;
  4["Map with BWA-MEM"];
  3 -->|output_paired_coll| 4;
  0 -->|output| 4;
  5["MarkDuplicates"];
  4 -->|bam_output| 5;
  6["Realign reads"];
  5 -->|outFile| 6;
  0 -->|output| 6;
  7["Samtools stats"];
  5 -->|outFile| 7;
  8["Insert indel qualities"];
  6 -->|realigned| 8;
  0 -->|output| 8;
  2ca7c89b-999f-41dc-8037-e54e25959a7e["Output\nRealigned Alignments with Indel Qualities"];
  8 --> 2ca7c89b-999f-41dc-8037-e54e25959a7e;
  style 2ca7c89b-999f-41dc-8037-e54e25959a7e stroke:#2c3143,stroke-width:4px;
  9["Call variants"];
  8 -->|output| 9;
  0 -->|output| 9;
  10["SnpEff eff:"];
  9 -->|variants| 10;
  11["SnpSift Extract Fields"];
  10 -->|snpeff_output| 11;
  06259137-eaa5-404a-923c-70ee5f1d89d4["Output\nSnpSift tabular output"];
  11 --> 06259137-eaa5-404a-923c-70ee5f1d89d4;
  style 06259137-eaa5-404a-923c-70ee5f1d89d4 stroke:#2c3143,stroke-width:4px;
  12["MultiQC"];
  3 -->|report_json| 12;
  7 -->|output| 12;
  5 -->|metrics_file| 12;
  10 -->|csvFile| 12;
  758ffde5-7ddd-482a-88b2-1504f8335488["Output\nMultiQC Report PE"];
  12 --> 758ffde5-7ddd-482a-88b2-1504f8335488;
  style 758ffde5-7ddd-482a-88b2-1504f8335488 stroke:#2c3143,stroke-width:4px;

Inputs

Outputs

Tools

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

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:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/sars-cov-2/workflows/main_workflow.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