SamestrGal

Run Workflow in Galaxy

• Galaxy Main
• Galaxy Canada
• Galaxy Europe
• Galaxy France
• Galaxy Australia
• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Collection\nRaw Reads"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Parameter\nSelect Host reference genome"];
  style 1 fill:#ded,stroke:#393,stroke-width:4px;
  2["ℹ️ Input Parameter\nSelect Sequencer for Trimmomatic"];
  style 2 fill:#ded,stroke:#393,stroke-width:4px;
  3["ℹ️ Input Parameter\nRun MetaPhlAn"];
  style 3 fill:#ded,stroke:#393,stroke-width:4px;
  4["ℹ️ Input Parameter\nSelect MetaPhlAn Database"];
  style 4 fill:#ded,stroke:#393,stroke-width:4px;
  5["ℹ️ Input Parameter\nSelect SameStr database"];
  style 5 fill:#ded,stroke:#393,stroke-width:4px;
  6["ℹ️ Input Parameter\nPercent identity"];
  style 6 fill:#ded,stroke:#393,stroke-width:4px;
  7["ℹ️ Input Parameter\nMinimum alignment length"];
  style 7 fill:#ded,stroke:#393,stroke-width:4px;
  8["ℹ️ Input Parameter\nMinimum base quality"];
  style 8 fill:#ded,stroke:#393,stroke-width:4px;
  9["ℹ️ Input Parameter\nMinimum alignment quality"];
  style 9 fill:#ded,stroke:#393,stroke-width:4px;
  10["ℹ️ Input Parameter\nMinimum vertical coverage"];
  style 10 fill:#ded,stroke:#393,stroke-width:4px;
  11["ℹ️ Input Parameter\nSameStr Filter: Minimum samples per clade"];
  style 11 fill:#ded,stroke:#393,stroke-width:4px;
  12["ℹ️ Input Parameter\nSameStr Filter: Marker truncation length"];
  style 12 fill:#ded,stroke:#393,stroke-width:4px;
  13["ℹ️ Input Parameter\nSameStr Filter: Nucleotides minimum variant coverage"];
  style 13 fill:#ded,stroke:#393,stroke-width:4px;
  14["ℹ️ Input Parameter\nSameStr Filter: Minimum variant coverage fraction"];
  style 14 fill:#ded,stroke:#393,stroke-width:4px;
  15["ℹ️ Input Parameter\nSameStr Filter: Minimum position coverage"];
  style 15 fill:#ded,stroke:#393,stroke-width:4px;
  16["ℹ️ Input Parameter\nSameStr Filter: Position coverage standard deviation cutoff"];
  style 16 fill:#ded,stroke:#393,stroke-width:4px;
  17["ℹ️ Input Parameter\nSameStr Filter: Minimum horizontal coverage"];
  style 17 fill:#ded,stroke:#393,stroke-width:4px;
  18["ℹ️ Input Parameter\nSameStr Filter: Minimum sample coverage per position"];
  style 18 fill:#ded,stroke:#393,stroke-width:4px;
  19["ℹ️ Input Parameter\nSameStr Summarize: Minimum overlap for comparison"];
  style 19 fill:#ded,stroke:#393,stroke-width:4px;
  20["ℹ️ Input Parameter\nSameStr Summarize: Minimum similarity for shared strains"];
  style 20 fill:#ded,stroke:#393,stroke-width:4px;
  21["Trimming and Host Removal"];
  1 -->|output| 21;
  0 -->|output| 21;
  2 -->|output| 21;
  22["Merge Collections"];
  21 -->|paired_output| 22;
  21 -->|unmatched_paired| 22;
  23["MetaPhlAn"];
  4 -->|output| 23;
  22 -->|output| 23;
  3 -->|output| 23;
  24["Pick parameter value"];
  23 -->|output_file| 24;
  25["Pick parameter value"];
  23 -->|sam_output_file| 25;
  26["Samtools view"];
  25 -->|data_param| 26;
  27["SameStr Convert"];
  26 -->|outputsam| 27;
  6 -->|output| 27;
  7 -->|output| 27;
  9 -->|output| 27;
  8 -->|output| 27;
  10 -->|output| 27;
  5 -->|output| 27;
  24 -->|data_param| 27;
  28["Flatten collection"];
  27 -->|npz_files| 28;
  29["Apply rules"];
  28 -->|output| 29;
  30["SameStr Merge"];
  5 -->|output| 30;
  29 -->|output| 30;
  31["SameStr Filter"];
  11 -->|output| 31;
  12 -->|output| 31;
  5 -->|output| 31;
  18 -->|output| 31;
  30 -->|sample_name| 31;
  30 -->|npz_files| 31;
  17 -->|output| 31;
  15 -->|output| 31;
  16 -->|output| 31;
  14 -->|output| 31;
  13 -->|output| 31;
  32["Filter empty datasets"];
  31 -->|filtered_profile| 32;
  33["Filter empty datasets"];
  31 -->|sample_names| 33;
  34["SameStr Stats"];
  5 -->|output| 34;
  33 -->|output| 34;
  32 -->|output| 34;
  677751a2-4e20-482e-a6d3-331c193c424f["Output\nstats file"];
  34 --> 677751a2-4e20-482e-a6d3-331c193c424f;
  style 677751a2-4e20-482e-a6d3-331c193c424f stroke:#2c3143,stroke-width:4px;
  35["SameStr Compare"];
  5 -->|output| 35;
  33 -->|output| 35;
  32 -->|output| 35;
  36["SameStr Summarize"];
  19 -->|output| 36;
  20 -->|output| 36;
  5 -->|output| 36;
  35 -->|overlap_file| 36;
  35 -->|fraction_file| 36;
  23 -->|output_file| 36;
  c85d67a8-ade1-4330-8339-224e6b70541c["Output\ncooccurrences"];
  36 --> c85d67a8-ade1-4330-8339-224e6b70541c;
  style c85d67a8-ade1-4330-8339-224e6b70541c stroke:#2c3143,stroke-width:4px;
  1ce03cd6-d170-49c1-a3f9-2700ea61fc63["Output\nstrain events"];
  36 --> 1ce03cd6-d170-49c1-a3f9-2700ea61fc63;
  style 1ce03cd6-d170-49c1-a3f9-2700ea61fc63 stroke:#2c3143,stroke-width:4px;
  e6a7aa1e-8eb6-410a-ae2d-f4a69883d891["Output\ntaxon counts"];
  36 --> e6a7aa1e-8eb6-410a-ae2d-f4a69883d891;
  style e6a7aa1e-8eb6-410a-ae2d-f4a69883d891 stroke:#2c3143,stroke-width:4px;

Inputs

Outputs

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

Hands On: Importing a workflow

1. Click on galaxy-workflows-activity Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
2. Click on galaxy-upload Import at the top-right of the screen
3. 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”
4. Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/samestr-strain-detection/workflows/samestr-strain-detection.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