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
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"]; 3["Samtools view"]; 4["Text transformation"]; 5["Samtools view"]; 6["TB-Profiler Profile"]; 7["Search in textfiles"]; 8["Add input name as column"]; 9["Concatenate datasets"]; 10["Replace Text"]; 0 -->|output| 2; 1 -->|output| 2; 2 -->|output| 3; 3 -->|outputsam| 4; 4 -->|output| 5; 5 -->|outputsam| 6; 6 -->|output_txt| 7; 7 -->|output| 8; 8 -->|output| 9; 9 -->|out_file1| 10;
From Fastqs to VCFs and BAMs
Last updated Mar 16, 2022
Launch in Tutorial Mode
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"]; 4["Trimmomatic"]; 5["snippy"]; 6["snippy"]; 7["Merge collections"]; 8["Merge collections"]; 9["TB Variant Filter"]; 0 -->|output| 3; 1 -->|output| 4; 3 -->|fastq_out| 5; 2 -->|output| 5; 4 -->|fastq_out_paired| 6; 2 -->|output| 6; 5 -->|snpvcf| 7; 6 -->|snpvcf| 7; 5 -->|snpsbam| 8; 6 -->|snpsbam| 8; 7 -->|output| 9;
From VCFs to SNP distance matrix
Last updated Mar 16, 2022
Launch in Tutorial Mode
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"]; 3["bcftools consensus"]; 4["Concatenate datasets"]; 5["Finds SNP sites"]; 6["SNP distance matrix"]; 0 -->|output| 2; 2 -->|output1| 3; 1 -->|output| 3; 3 -->|output_file| 4; 4 -->|out_file1| 5; 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: