From BAMs to drug resistance prediction with TB-profiler

evolution-mtb_transmission/galaxy-workflow-from-bams-to-drug-resistance-prediction-with-tb-profiler

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:W00074
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\nMTB single-end BAMs"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Collection\nMTB paired-end BAMs"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Merge collections"];
  0 -->|output| 2;
  1 -->|output| 2;
  3["Samtools view BAM > SAM"];
  2 -->|output| 3;
  aa220027-9d10-4328-b2c2-e4d139d5d5bd["Output\nSamtools view on input dataset(s): filtered alignments"];
  3 --> aa220027-9d10-4328-b2c2-e4d139d5d5bd;
  style aa220027-9d10-4328-b2c2-e4d139d5d5bd stroke:#2c3143,stroke-width:4px;
  4["Sed MTB_anc to Chromosome"];
  3 -->|outputsam| 4;
  5["Samtools view SAM > BAM"];
  4 -->|output| 5;
  6["TB-profiler"];
  5 -->|outputsam| 6;
  7["Get drug resistance profile"];
  6 -->|output_txt| 7;
  8["Add Sample Name"];
  7 -->|output| 8;
  9["Concatenate DR profiles in a single table"];
  8 -->|output| 9;
  10["Cleanup the table"];
  9 -->|out_file1| 10;

Inputs

Input Label
Input dataset collection MTB single-end BAMs
Input dataset collection MTB paired-end BAMs

Outputs

From Output Label
__MERGE_COLLECTION__ Merge collections Merge collections
toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.13+galaxy2 Samtools view Samtools view BAM > SAM
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1 Text transformation Sed (MTB_anc to Chromosome)
toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.13+galaxy2 Samtools view Samtools view SAM > BAM
toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/3.0.8+galaxy0 TB-Profiler Profile TB-profiler
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1 Search in textfiles Get drug resistance profile
toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0 Add input name as column Add Sample Name
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1 Concatenate datasets Concatenate DR profiles in a single table
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2 Replace Text Cleanup the table

Tools

Tool Links
__MERGE_COLLECTION__
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1 View in ToolShed
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/bgruening/text_processing/tp_sed_tool/1.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.13+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/3.0.8+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0 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 103d41943 2022-03-16 09:29:31 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_BAMs_to_drug_resistance_prediction_with_TB-profiler.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