Allele-based Pathogen Identification

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Collection\ncollection_of_preprocessed_samples"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Parameter\nsamples_profile"];
  style 1 fill:#ded,stroke:#393,stroke-width:4px;
  2["ℹ️ Input Dataset\nreference_genome_of_tested_strain"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Convert compressed file to uncompressed."];
  2 -->|output| 3;
  9d6bde4a-7180-4097-9ffd-6992111a617c["Output\ndecompressed_rg_file"];
  3 --> 9d6bde4a-7180-4097-9ffd-6992111a617c;
  style 9d6bde4a-7180-4097-9ffd-6992111a617c stroke:#2c3143,stroke-width:4px;
  4["Map with minimap2"];
  1 -->|output| 4;
  0 -->|output| 4;
  3 -->|output1| 4;
  31779c23-4f26-418e-9418-2551e883dbe7["Output\nmap_with_minimap2"];
  4 --> 31779c23-4f26-418e-9418-2551e883dbe7;
  style 31779c23-4f26-418e-9418-2551e883dbe7 stroke:#2c3143,stroke-width:4px;
  5["Clair3"];
  4 -->|alignment_output| 5;
  3 -->|output1| 5;
  1cf1ee6c-4cb7-45e3-9c7b-88a1b678dd53["Output\nclair3_pileup_vcf"];
  5 --> 1cf1ee6c-4cb7-45e3-9c7b-88a1b678dd53;
  style 1cf1ee6c-4cb7-45e3-9c7b-88a1b678dd53 stroke:#2c3143,stroke-width:4px;
  987f9145-83ab-44f1-801a-b0d527ecbce8["Output\nclair3_full_alignment_vcf"];
  5 --> 987f9145-83ab-44f1-801a-b0d527ecbce8;
  style 987f9145-83ab-44f1-801a-b0d527ecbce8 stroke:#2c3143,stroke-width:4px;
  fab82215-f59a-43b1-92d7-37629a1fdb65["Output\nclair3_merged_output"];
  5 --> fab82215-f59a-43b1-92d7-37629a1fdb65;
  style fab82215-f59a-43b1-92d7-37629a1fdb65 stroke:#2c3143,stroke-width:4px;
  6["Samtools depth"];
  4 -->|alignment_output| 6;
  7["Samtools coverage"];
  4 -->|alignment_output| 7;
  8["bcftools norm"];
  5 -->|merge_output| 8;
  3 -->|output1| 8;
  22553aa1-f5db-4d37-87c4-1164dbb3d2d5["Output\nnormalized_vcf_output"];
  8 --> 22553aa1-f5db-4d37-87c4-1164dbb3d2d5;
  style 22553aa1-f5db-4d37-87c4-1164dbb3d2d5 stroke:#2c3143,stroke-width:4px;
  9["Advanced Cut"];
  6 -->|output| 9;
  10["Remove beginning"];
  7 -->|output| 10;
  11["SnpSift Filter"];
  8 -->|output_file| 11;
  3e7981ec-2205-4571-93eb-10c0dd14b288["Output\nquality_filtered_vcf_output"];
  11 --> 3e7981ec-2205-4571-93eb-10c0dd14b288;
  style 3e7981ec-2205-4571-93eb-10c0dd14b288 stroke:#2c3143,stroke-width:4px;
  12["Table Compute"];
  9 -->|output| 12;
  13["Cut"];
  10 -->|out_file1| 13;
  14["SnpSift Extract Fields"];
  11 -->|output| 14;
  1b0f4f2c-4717-45be-b580-fe10cba78c35["Output\nextracted_fields_from_the_vcf_output"];
  14 --> 1b0f4f2c-4717-45be-b580-fe10cba78c35;
  style 1b0f4f2c-4717-45be-b580-fe10cba78c35 stroke:#2c3143,stroke-width:4px;
  15["bcftools consensus"];
  11 -->|output| 15;
  3 -->|output1| 15;
  49497f3c-9332-4924-bcfd-cb71788ad2c2["Output\nbcftools_consensus"];
  15 --> 49497f3c-9332-4924-bcfd-cb71788ad2c2;
  style 49497f3c-9332-4924-bcfd-cb71788ad2c2 stroke:#2c3143,stroke-width:4px;
  16["Select first"];
  13 -->|out_file1| 16;
  17["Remove beginning"];
  14 -->|output| 17;
  18["Collapse Collection"];
  16 -->|outfile| 18;
  5ee1c158-1a85-45ca-9abd-b30632b3092c["Output\nmapping_coverage_percentage_per_sample"];
  18 --> 5ee1c158-1a85-45ca-9abd-b30632b3092c;
  style 5ee1c158-1a85-45ca-9abd-b30632b3092c stroke:#2c3143,stroke-width:4px;
  19["Count"];
  17 -->|out_file1| 19;
  20["Advanced Cut"];
  18 -->|output| 20;
  21["Cut"];
  19 -->|out_file1| 21;
  22["Paste"];
  20 -->|output| 22;
  12 -->|table| 22;
  25b7b87b-5ef1-487f-90cc-81351a2f81ce["Output\nmapping_mean_depth_per_sample"];
  22 --> 25b7b87b-5ef1-487f-90cc-81351a2f81ce;
  style 25b7b87b-5ef1-487f-90cc-81351a2f81ce stroke:#2c3143,stroke-width:4px;
  23["Select first"];
  21 -->|out_file1| 23;
  24["Collapse Collection"];
  23 -->|outfile| 24;
  25["Column Regex Find And Replace"];
  24 -->|output| 25;
  2852c4ee-24ea-4df7-b59e-54eb6e2f470b["Output\nnumber_of_variants_per_sample"];
  25 --> 2852c4ee-24ea-4df7-b59e-54eb6e2f470b;
  style 2852c4ee-24ea-4df7-b59e-54eb6e2f470b stroke:#2c3143,stroke-width:4px;

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

• 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:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/workflows/allele_based_pathogen_identification.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