Workflows

These workflows are associated with Removal of human reads from SARS-CoV-2 sequencing data

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.

GTN - Sequence Analyses - Removal of human reads from SARS-CoV-2 sequencing data

Last updated Aug 4, 2021

Launch in Tutorial Mode
License: None Specified, defaults to CC-BY-4.0
Tests: ❌ Results: Not yet automated

Download Galaxy Workflow.ga Galaxy Europe Galaxy Australia Galaxy France Galaxy Main Import to another server (≥23.0+ only!) 
flowchart TD
  0["ℹ️ Input Collection\nInput Dataset Collection"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Trimmomatic"];
  0 -->|output| 1;
  2["Unzip Collection"];
  0 -->|output| 2;
  3["Map with BWA-MEM"];
  1 -->|fastq_out_paired| 3;
  4["Samtools fastx"];
  3 -->|bam_output| 4;
  5["Select"];
  4 -->|forward| 5;
  6["Replace Text"];
  5 -->|out_file1| 6;
  7["seqtk_subseq"];
  2 -->|forward| 7;
  6 -->|outfile| 7;
  8["seqtk_subseq"];
  2 -->|reverse| 8;
  6 -->|outfile| 8;
  9["Paired-end collection of cleaned reads"];
  7 -->|default| 9;
  8 -->|default| 9;
  f24bbf28-dc51-440f-a758-ac05033f0645["Output\nCleaned Data"];
  9 --> f24bbf28-dc51-440f-a758-ac05033f0645;
  style f24bbf28-dc51-440f-a758-ac05033f0645 stroke:#2c3143,stroke-width:4px;

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