Simple COVID-19 - PE Variation

variant-analysis-sars-cov-2/main-workflow

Author(s)

Version
7
Last updated
Jun 24, 2020
License
None Specified, defaults to CC-BY-4.0
Tags
variant-analysis

Features
Tutorial
From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00266
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode
Download 
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;

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 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
7 18338ab9a 2020-06-24 13:27:11 Use correct fasterqdump version
6 979d6cd21 2020-06-24 13:12:17 Reformat workflow, bump lofreq to 2.1.5
5 ced05a792 2020-06-23 20:38:10 Fix workflow connections
4 1c38a3ed2 2020-06-23 20:10:19 Use newer, simpler output
3 a58450027 2020-06-22 15:06:56 add topic tag to workflow
2 e8eea0705 2020-06-22 14:24:44 reformat workflow
1 a06c40264 2020-06-17 10:30:14 Skeleton from PE sars-cov-2 workflow

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