GigaScience-RNAseq-Optitype-seq2HLA-to-IEDB-alleles

proteomics-neoantigen-6-predicting-hla-binding/main-workflow

Author(s)
galaxyp
Version
1
Last updated
Jan 14, 2025
License
GPL-3.0-or-later
Tags
HLA
name:neoantigen

Features
Tutorial
Neoantigen 6: Predicting HLA Binding
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00303
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nR1.fastq"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nR2.fastq"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Optitype"];
  0 -->|output| 2;
  1 -->|output| 2;
  cce6a623-1f69-47f9-af17-f6d147bc6494["Output\nOptiType_on_input_datasets_result"];
  2 --> cce6a623-1f69-47f9-af17-f6d147bc6494;
  style cce6a623-1f69-47f9-af17-f6d147bc6494 stroke:#2c3143,stroke-width:4px;
  c3aeb7f3-89e2-4b9b-b8af-481955d7de61["Output\nOptiType_on_input_datasets_coverage_plot"];
  2 --> c3aeb7f3-89e2-4b9b-b8af-481955d7de61;
  style c3aeb7f3-89e2-4b9b-b8af-481955d7de61 stroke:#2c3143,stroke-width:4px;
  3["seq2HLA"];
  0 -->|output| 3;
  1 -->|output| 3;
  be8e1b19-4a02-4d37-b716-355aac3466d6["Output\nseq2HLA_genotype_4digits"];
  3 --> be8e1b19-4a02-4d37-b716-355aac3466d6;
  style be8e1b19-4a02-4d37-b716-355aac3466d6 stroke:#2c3143,stroke-width:4px;
  4["Reformated-Optitype-Data"];
  2 -->|result| 4;
  b359062d-bb66-4ad6-a4fe-a80c71671a6a["Output\nReformated-Optitype-Data"];
  4 --> b359062d-bb66-4ad6-a4fe-a80c71671a6a;
  style b359062d-bb66-4ad6-a4fe-a80c71671a6a stroke:#2c3143,stroke-width:4px;
  5["IEDB_alleles"];
  4 -->|outfile| 5;
  3 -->|c1_genotype4digits| 5;
  865da3d9-67ed-44ef-b019-f489ad834188["Output\nIEDB_Optitype_alleles"];
  5 --> 865da3d9-67ed-44ef-b019-f489ad834188;
  style 865da3d9-67ed-44ef-b019-f489ad834188 stroke:#2c3143,stroke-width:4px;
  e7f83293-69fa-44c9-9627-904c2b0dde97["Output\nIEDB-Optitype-seq2HLA-alleles"];
  5 --> e7f83293-69fa-44c9-9627-904c2b0dde97;
  style e7f83293-69fa-44c9-9627-904c2b0dde97 stroke:#2c3143,stroke-width:4px;
  cc73bee6-39bd-44d3-915c-ef38d15fe3af["Output\nIEDB_seq2HLA_alleles"];
  5 --> cc73bee6-39bd-44d3-915c-ef38d15fe3af;
  style cc73bee6-39bd-44d3-915c-ef38d15fe3af stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset R1.fastq
Input dataset R2.fastq

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/optitype/optitype/1.3.5+galaxy0 OptiType Optitype
toolshed.g2.bx.psu.edu/repos/iuc/seq2hla/seq2hla/2.3+galaxy0 seq2HLA seq2HLA
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1 Text reformatting Reformated-Optitype-Data
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2 Query Tabular IEDB_alleles

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/optitype/optitype/1.3.5+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/seq2hla/seq2hla/2.3+galaxy0 View in ToolShed

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 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
1 6e4ce4916 2024-11-14 15:41:21 Made sure the order is right

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/neoantigen-6-predicting-hla-binding/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