Workflows

These workflows are associated with Identifying tuberculosis transmission links: from SNPs to transmission clusters

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.

From BAMs to drug resistance prediction with TB-profiler

Last updated Mar 16, 2022

Launch in Tutorial Mode question
License: None Specified, defaults to CC-BY-4.0
Tests: ❌ Results: Not yet automated

flowchart TD
  0["Input dataset collection"];
  1["Input dataset collection"];
  2["Merge collections"];
  0 -->|output| 2;
  1 -->|output| 2;
  3["Samtools view"];
  2 -->|output| 3;
  4["Text transformation"];
  3 -->|outputsam| 4;
  5["Samtools view"];
  4 -->|output| 5;
  6["TB-Profiler Profile"];
  5 -->|outputsam| 6;
  7["Search in textfiles"];
  6 -->|output_txt| 7;
  8["Add input name as column"];
  7 -->|output| 8;
  9["Concatenate datasets"];
  8 -->|output| 9;
  10["Replace Text"];
  9 -->|out_file1| 10;

	
From Fastqs to VCFs and BAMs

Last updated Mar 16, 2022

Launch in Tutorial Mode question
License: None Specified, defaults to CC-BY-4.0
Tests: ❌ Results: Not yet automated

flowchart TD
  0["Input dataset collection"];
  1["Input dataset collection"];
  2["Input dataset"];
  3["Trimmomatic"];
  0 -->|output| 3;
  4["Trimmomatic"];
  1 -->|output| 4;
  5["snippy"];
  3 -->|fastq_out| 5;
  2 -->|output| 5;
  6["snippy"];
  4 -->|fastq_out_paired| 6;
  2 -->|output| 6;
  7["Merge collections"];
  5 -->|snpvcf| 7;
  6 -->|snpvcf| 7;
  8["Merge collections"];
  5 -->|snpsbam| 8;
  6 -->|snpsbam| 8;
  9["TB Variant Filter"];
  7 -->|output| 9;

	
From VCFs to SNP distance matrix

Last updated Mar 16, 2022

Launch in Tutorial Mode question
License: None Specified, defaults to CC-BY-4.0
Tests: ❌ Results: Not yet automated

flowchart TD
  0["Input dataset collection"];
  1["Input dataset"];
  2["TB Variant Filter"];
  0 -->|output| 2;
  3["bcftools consensus"];
  2 -->|output1| 3;
  1 -->|output| 3;
  4["Concatenate datasets"];
  3 -->|output_file| 4;
  5["Finds SNP sites"];
  4 -->|out_file1| 5;
  6["SNP distance matrix"];
  5 -->|output_fasta| 6;

	

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: