GigaScience_Peptide_Annotation_demonstration_STS26T_neoantigen_candidates_workflow

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nNovel_Peptides"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nFragpipe-Peptide-Report"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nAnnotated-GffCompared-GTFtoBED"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nHomo_sapiens.GRCh38_canon.106.gtf"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["Peptide_to_Protein_Annotation"];
  0 -->|output| 4;
  1 -->|output| 4;
  4631011c-b1d4-4964-96d6-5a11201afb75["Output\nPeptide_to_Protein_Annotation"];
  4 --> 4631011c-b1d4-4964-96d6-5a11201afb75;
  style 4631011c-b1d4-4964-96d6-5a11201afb75 stroke:#2c3143,stroke-width:4px;
  5["FASTA-IEDB"];
  4 -->|output| 5;
  3b728452-3d59-4e5f-a9dc-8764ceb60094["Output\nFASTA-IEDB"];
  5 --> 3b728452-3d59-4e5f-a9dc-8764ceb60094;
  style 3b728452-3d59-4e5f-a9dc-8764ceb60094 stroke:#2c3143,stroke-width:4px;
  6["Converting_pipes_to_columns"];
  4 -->|output| 6;
  58ea288e-1160-4617-8207-453bf29b0d12["Output\nTable-processing-1"];
  6 --> 58ea288e-1160-4617-8207-453bf29b0d12;
  style 58ea288e-1160-4617-8207-453bf29b0d12 stroke:#2c3143,stroke-width:4px;
  7["Modifying-string-name"];
  6 -->|out_file1| 7;
  a607fb3f-2e87-410a-9dfb-9286baf667e9["Output\nModified-string-name"];
  7 --> a607fb3f-2e87-410a-9dfb-9286baf667e9;
  style a607fb3f-2e87-410a-9dfb-9286baf667e9 stroke:#2c3143,stroke-width:4px;
  8["Converting_colons_to_columns"];
  7 -->|out_file1| 8;
  e24ff14e-b512-4444-9abb-b3c46d4fb707["Output\nTable-processing-2"];
  8 --> e24ff14e-b512-4444-9abb-b3c46d4fb707;
  style e24ff14e-b512-4444-9abb-b3c46d4fb707 stroke:#2c3143,stroke-width:4px;
  9["Extracting-info-from-GFFtobed"];
  8 -->|out_file1| 9;
  2 -->|output| 9;
  e78166a9-a99b-429d-b01e-e5e19084e1c0["Output\nExtracting-info-from-GFFtobed"];
  9 --> e78166a9-a99b-429d-b01e-e5e19084e1c0;
  style e78166a9-a99b-429d-b01e-e5e19084e1c0 stroke:#2c3143,stroke-width:4px;
  10["Table-processing-3"];
  9 -->|output| 10;
  734962f8-efbf-4b30-a00b-0293b098eb68["Output\nTable-processing-3"];
  10 --> 734962f8-efbf-4b30-a00b-0293b098eb68;
  style 734962f8-efbf-4b30-a00b-0293b098eb68 stroke:#2c3143,stroke-width:4px;
  11["Peptide-location-generation"];
  10 -->|output| 11;
  0d9f1cbf-fa72-42c1-ab78-4faa5e123bb1["Output\nPeptide-location-generation"];
  11 --> 0d9f1cbf-fa72-42c1-ab78-4faa5e123bb1;
  style 0d9f1cbf-fa72-42c1-ab78-4faa5e123bb1 stroke:#2c3143,stroke-width:4px;
  12["BED-File-for-PepPointer"];
  11 -->|output| 12;
  3970ec24-eb99-459f-8bb4-bc3b69faaca9["Output\nBED-File-for-PepPointer"];
  12 --> 3970ec24-eb99-459f-8bb4-bc3b69faaca9;
  style 3970ec24-eb99-459f-8bb4-bc3b69faaca9 stroke:#2c3143,stroke-width:4px;
  13["PepPointer"];
  12 -->|output| 13;
  3 -->|output| 13;
  ee5ad6db-d9d4-4ae4-9d69-c37ccb3f4475["Output\nPepPointer-Annotated-Peptides"];
  13 --> ee5ad6db-d9d4-4ae4-9d69-c37ccb3f4475;
  style ee5ad6db-d9d4-4ae4-9d69-c37ccb3f4475 stroke:#2c3143,stroke-width:4px;
  14["Summary-Neoantigen"];
  13 -->|classified| 14;
  dbcedf04-dffe-49bc-bac5-a3ef2d41fabd["Output\nNeoantigen_summary"];
  14 --> dbcedf04-dffe-49bc-bac5-a3ef2d41fabd;
  style dbcedf04-dffe-49bc-bac5-a3ef2d41fabd 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

• 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/proteomics/tutorials/neoantigen-5-variant-annotation/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