TB Variant Analysis v1.0
variant-analysis-tb-variant-analysis/tb-variant-analysis
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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;
Inputs
Input | Label |
---|---|
Input dataset collection | Reads |
Input dataset | Reference Genome |
Input parameter | Minimum depth of coverage |
Input parameter | Minimum variant allele frequency |
Input parameter | Additional BWA-MEM options |
Outputs
From | Output | Label |
---|---|---|
toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1 | Kraken2 | |
toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/6.2.1+galaxy0 | TB-Profiler Profile | |
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1 | Text transformation | |
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1 | MultiQC | |
toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3 | bcftools consensus | |
toolshed.g2.bx.psu.edu/repos/iuc/tbvcfreport/tbvcfreport/1.0.0+galaxy0 | TB Variant Report |
Tools
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 galaxy-upload 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