TB Variant Analysis v1.0

variant-analysis-tb-variant-analysis/tb-variant-analysis

Author(s)
Peter van Heusden
Version
14
Last updated
Jun 10, 2024
License
AGPL-3.0-or-later
Tags
pathogen
tuberculosis

Features
Tutorial
M. tuberculosis Variant Analysis
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00269
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\nReads"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nReference Genome"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Parameter\nMinimum depth of coverage"];
  style 2 fill:#ded,stroke:#393,stroke-width:4px;
  3["ℹ️ Input Parameter\nMinimum variant allele frequency"];
  style 3 fill:#ded,stroke:#393,stroke-width:4px;
  4["ℹ️ Input Parameter\nAdditional BWA-MEM options"];
  style 4 fill:#ded,stroke:#393,stroke-width:4px;
  5["fastp"];
  0 -->|output| 5;
  6["seqret"];
  1 -->|output| 6;
  7["snippy"];
  4 -->|output| 7;
  2 -->|output| 7;
  3 -->|output| 7;
  5 -->|output_paired_coll| 7;
  1 -->|output| 7;
  8["Kraken2"];
  5 -->|output_paired_coll| 8;
  c7abf2bf-ed4c-433e-a695-9eca61282bb5["Output\nreport_output"];
  8 --> c7abf2bf-ed4c-433e-a695-9eca61282bb5;
  style c7abf2bf-ed4c-433e-a695-9eca61282bb5 stroke:#2c3143,stroke-width:4px;
  083a0e51-7780-4c91-a071-dc0e4641d060["Output\noutput"];
  8 --> 083a0e51-7780-4c91-a071-dc0e4641d060;
  style 083a0e51-7780-4c91-a071-dc0e4641d060 stroke:#2c3143,stroke-width:4px;
  9["QualiMap BamQC"];
  7 -->|snpsbam| 9;
  10["mosdepth"];
  2 -->|output| 10;
  7 -->|snpsbam| 10;
  11["TB Variant Filter"];
  7 -->|snpvcf| 11;
  12["TB-Profiler Profile"];
  7 -->|snpsbam| 12;
  335635b4-a4de-4980-ad02-68f0035daeaa["Output\noutput_txt"];
  12 --> 335635b4-a4de-4980-ad02-68f0035daeaa;
  style 335635b4-a4de-4980-ad02-68f0035daeaa stroke:#2c3143,stroke-width:4px;
  13["TB Variant Filter"];
  7 -->|snpvcf| 13;
  14["Flatten collection"];
  9 -->|raw_data| 14;
  15["Text reformatting"];
  10 -->|output_quantized_bed| 15;
  16["Text transformation"];
  11 -->|output1| 16;
  007df8c2-bd13-495f-8904-abf31d4594d0["Output\nFinal annotated VCF"];
  16 --> 007df8c2-bd13-495f-8904-abf31d4594d0;
  style 007df8c2-bd13-495f-8904-abf31d4594d0 stroke:#2c3143,stroke-width:4px;
  17["MultiQC"];
  5 -->|report_json| 17;
  14 -->|output| 17;
  59528235-7525-4ef9-8810-36f1ed0f01f6["Output\nhtml_report"];
  17 --> 59528235-7525-4ef9-8810-36f1ed0f01f6;
  style 59528235-7525-4ef9-8810-36f1ed0f01f6 stroke:#2c3143,stroke-width:4px;
  18["bcftools consensus"];
  13 -->|output1| 18;
  6 -->|out_file1| 18;
  15 -->|outfile| 18;
  c71b135d-35f9-44d0-a20e-f25528e518af["Output\nconsensus_genome"];
  18 --> c71b135d-35f9-44d0-a20e-f25528e518af;
  style c71b135d-35f9-44d0-a20e-f25528e518af stroke:#2c3143,stroke-width:4px;
  19["TB Variant Report"];
  16 -->|output| 19;
  12 -->|results_json| 19;
  959528d2-f8f2-4440-99cf-44fddd6c5069["Output\ndrug_resistance_report_html"];
  19 --> 959528d2-f8f2-4440-99cf-44fddd6c5069;
  style 959528d2-f8f2-4440-99cf-44fddd6c5069 stroke:#2c3143,stroke-width:4px;
  4d9636eb-075b-4fd2-a1e4-1a7c37a17fc0["Output\nvariants_report_html"];
  19 --> 4d9636eb-075b-4fd2-a1e4-1a7c37a17fc0;
  style 4d9636eb-075b-4fd2-a1e4-1a7c37a17fc0 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
14 c0042e7f3 2024-06-10 13:19:51 Update to address comments from wm
13 01cf3d5e2 2024-06-07 19:26:49 Add snippers for running workflow from workflowhub.eu and jbrowse vis
12 d3db4cd3e 2024-06-07 14:40:37 Update the M. tuberculosis variant analysis tutorial * Update all tools to latest versions * Change to fastp instead of Trimmomatic * Add section on running workflow * Update workflow and workflow test
11 d61d5645f 2023-09-25 12:08:06 Update tb_variant_filter to v. 0.4.0
10 c89f11fe3 2023-04-27 19:45:53 Update some tools in tuberculosis variant analysis tutorial (#4070)
9 fa9e9fb00 2023-01-01 09:42:09 New variant of tb_variant_filter and tbprofiler, more detail on tb_variant_filter
8 6e9c1860b 2022-03-23 15:19:25 Restore workflow indentation and fix WF step order
7 354e9edf1 2022-03-23 09:43:15 Use correct snippy wrapper version everywhere
6 6f476a032 2022-03-22 19:17:28 Update snippy to 4.6.0
5 946f6f60f 2022-03-22 08:34:11 Generate cleaner intermediate diff
4 8e46a42b5 2022-03-22 06:04:22 Autoupdate workflow, change Kraken2 test
3 f98407ff4 2020-07-25 21:45:23 tb-variant-analysis: label workflow outputs and add test
2 392830f9b 2020-07-25 20:02:29 Reformat tb-variant-analysis workflow
1 2e73bb7aa 2020-07-25 19:32:51 Update M. tuberculosis variant analysis tutorial with new data and workflow

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/tb-variant-analysis/workflows/tb-variant-analysis.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