From VCFs to SNP distance matrix
evolution-mtb_transmission/main-workflow
Launch in Tutorial Mode
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flowchart TD 0["ℹ️ Input Collection\nCollection of VCFs to analyze"]; style 0 stroke:#2c3143,stroke-width:4px; 1["ℹ️ Input Dataset\nReference genome of the MTBC ancestor"]; style 1 stroke:#2c3143,stroke-width:4px; 2["Filter TB variants"]; 0 -->|output| 2; 3["Generate the complete genome of each of the samples"]; 2 -->|output1| 3; 1 -->|output| 3; ce5dd7a2-c33d-46b4-9f02-68c2bdfcf31a["Output\n#{input_file}"]; 3 --> ce5dd7a2-c33d-46b4-9f02-68c2bdfcf31a; style ce5dd7a2-c33d-46b4-9f02-68c2bdfcf31a stroke:#2c3143,stroke-width:4px; 4["Concatenate genomes to build a MSA"]; 3 -->|output_file| 4; 5["Keep only variable positions"]; 4 -->|out_file1| 5; 6["Calculate SNP distances"]; 5 -->|output_fasta| 6;
Inputs
Input | Label |
---|---|
Input dataset collection | Collection of VCFs to analyze |
Input dataset | Reference genome of the MTBC ancestor |
Outputs
From | Output | Label |
---|---|---|
toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.1.3+galaxy0 | TB Variant Filter | Filter TB variants |
toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.9+galaxy2 | bcftools consensus | Generate the complete genome of each of the samples |
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1 | Concatenate datasets | Concatenate genomes to build a MSA |
toolshed.g2.bx.psu.edu/repos/iuc/snp_sites/snp_sites/2.5.1+galaxy0 | Finds SNP sites | Keep only variable positions |
toolshed.g2.bx.psu.edu/repos/iuc/snp_dists/snp_dists/0.6.3+galaxy0 | SNP distance matrix | Calculate SNP distances |
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 |
---|---|---|---|
2 | 679ca224e | 2022-03-16 09:30:16 | 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/main_workflow.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