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

sequence-analysis-human-reads-removal/human-reads-removal

Author(s)

Version
1
Last updated
Aug 4, 2021
License
None Specified, defaults to CC-BY-4.0
Tags
sequence-analysis

Features
Tutorial
Removal of human reads from SARS-CoV-2 sequencing data
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00180
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 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;

Inputs

Input Label
Input dataset collection Input Dataset Collection

Outputs

From Output Label
Input dataset collection Input Dataset Collection
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1 Trimmomatic
__UNZIP_COLLECTION__ Unzip Collection
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2 Map with BWA-MEM
toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1 Samtools fastx
Grep1 Select
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2 Replace Text
toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1 seqtk_subseq
toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1 seqtk_subseq
__ZIP_COLLECTION__ Zip Collection Paired-end collection of cleaned reads

Tools

Tool Links
Grep1
__UNZIP_COLLECTION__
__ZIP_COLLECTION__
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1 View in ToolShed

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
2 f71f6dde0 2021-08-03 17:42:59 Address WF linting issues
1 f232ad426 2021-08-03 17:10:49 Add new tutorial for cleaning SARS-CoV-2 data

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/human-reads-removal/workflows/human-reads-removal.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