From Fastqs to VCFs and BAMs

evolution-mtb_transmission/galaxy-workflow-from-fastqs-to-vcfs-and-bams

Author(s)

Version
1
Last updated
Mar 16, 2022
License
None Specified, defaults to CC-BY-4.0
Tags
evolution

Features
Tutorial
Identifying tuberculosis transmission links: from SNPs to transmission clusters
Other workflows associated with this material
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00075
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Collection\nSingle-End FASTQs"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Collection\nPaired-End FASTQs"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nMycobacterium_tuberculosis_ancestral_reference.gbk"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Trimmomatic"];
  0 -->|output| 3;
  4["Trimmomatic"];
  1 -->|output| 4;
  5["Mapping and variant calling of SINGLE END FASTQs with snippy"];
  3 -->|fastq_out| 5;
  2 -->|output| 5;
  6["Mapping and variant calling of PAIRED END FASTQs with snippy"];
  4 -->|fastq_out_paired| 6;
  2 -->|output| 6;
  7["Merge PE/SE VCFs in a single collection with all samples"];
  5 -->|snpvcf| 7;
  6 -->|snpvcf| 7;
  8["Merge PE/SE BAMs in a single collection with all samples Part the workflow ”Identifying DR with TB-profiler"];
  5 -->|snpsbam| 8;
  6 -->|snpsbam| 8;
  9["TB Variant Filter"];
  7 -->|output| 9;

Inputs

Input Label
Input dataset collection Single-End FASTQs
Input dataset collection Paired-End FASTQs
Input dataset Mycobacterium_tuberculosis_ancestral_reference.gbk

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1 Trimmomatic
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1 Trimmomatic
toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2 snippy Mapping and variant calling of SINGLE END FASTQs with snippy
toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.6.0+galaxy0 snippy Mapping and variant calling of PAIRED END FASTQs with snippy
__MERGE_COLLECTION__ Merge collections Merge PE/SE VCFs in a single collection with all samples
toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.3.5+galaxy2 TB Variant Filter

Tools

Tool Links
__MERGE_COLLECTION__
toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.6.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.3.5+galaxy2 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 61e538363 2022-03-16 09:30:11 update tag
1 2e7ba7852 2022-03-16 09:24:13 tweak

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/evolution/tutorials/mtb_transmission/workflows/Galaxy-Workflow-From_Fastqs_to_VCFs_and_BAMs.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