GigaScience_Database_merge_FragPipe_STS26T_demonstration

proteomics-neoantigen-fragpipe-discovery/main-workflow

Author(s)
GalaxyP
Version
1
Last updated
Jul 2, 2025
License
CC-BY-4.0
Tags
name:neoantigen

Features
Tutorial
Neoantigen 2: Database merge and FragPipe discovery
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00340
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nHuman_cRAP_Non_normal_transcripts_dB"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nFusion-database"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nInput-RAW-FILE"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nFragPipe_Experimental_design_tabular"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["Merge_non-normal_fusion_FASTA-files"];
  0 -->|output| 4;
  1 -->|output| 4;
  19df6de4-6440-4693-b893-139213d4e07e["Output\nNon_normal_and_Fusion_dB"];
  4 --> 19df6de4-6440-4693-b893-139213d4e07e;
  style 19df6de4-6440-4693-b893-139213d4e07e stroke:#2c3143,stroke-width:4px;
  5["Validation_of_Fasta_file"];
  4 -->|output| 5;
  efefe5f3-7bb9-42fe-a39b-b220fcaf1add["Output\nValidated-fasta"];
  5 --> efefe5f3-7bb9-42fe-a39b-b220fcaf1add;
  style efefe5f3-7bb9-42fe-a39b-b220fcaf1add stroke:#2c3143,stroke-width:4px;
  6["Fragpipe"];
  5 -->|goodFastaOut| 6;
  2 -->|output| 6;
  3 -->|output| 6;
  80182cb4-4a70-4a50-a42f-0de196f6e95b["Output\nFragpipe_output_peptide"];
  6 --> 80182cb4-4a70-4a50-a42f-0de196f6e95b;
  style 80182cb4-4a70-4a50-a42f-0de196f6e95b stroke:#2c3143,stroke-width:4px;
  6e4e993f-8d69-4008-9528-91ea2699ab02["Output\nFragpipe_output_protein"];
  6 --> 6e4e993f-8d69-4008-9528-91ea2699ab02;
  style 6e4e993f-8d69-4008-9528-91ea2699ab02 stroke:#2c3143,stroke-width:4px;
  b1ac88a6-70fb-4a0c-bc52-aa4f37019c8d["Output\nFragpipe_output_psm"];
  6 --> b1ac88a6-70fb-4a0c-bc52-aa4f37019c8d;
  style b1ac88a6-70fb-4a0c-bc52-aa4f37019c8d stroke:#2c3143,stroke-width:4px;
  7["Extract_Peptides_from_Fragpipe"];
  6 -->|output_peptide| 7;
  a3548299-ee6a-4649-a741-0e934557daf3["Output\nFragpipe-Peptide-Report"];
  7 --> a3548299-ee6a-4649-a741-0e934557daf3;
  style a3548299-ee6a-4649-a741-0e934557daf3 stroke:#2c3143,stroke-width:4px;
  8["Removing_known_human_peptides"];
  7 -->|output| 8;
  275b4fb5-e4c2-48ce-a8d8-92c91b1831fc["Output\nRemoving_known_human_peptides"];
  8 --> 275b4fb5-e4c2-48ce-a8d8-92c91b1831fc;
  style 275b4fb5-e4c2-48ce-a8d8-92c91b1831fc stroke:#2c3143,stroke-width:4px;
  9["Extracting_Peptide-Candidates"];
  8 -->|out_file1| 9;
  443d70da-5732-449a-89fb-c8fc094dbaee["Output\nExtracting_Peptide-Candidates"];
  9 --> 443d70da-5732-449a-89fb-c8fc094dbaee;
  style 443d70da-5732-449a-89fb-c8fc094dbaee stroke:#2c3143,stroke-width:4px;
  10["Neoantigen_Peptide_Candidates_for_PepQuery"];
  9 -->|output| 10;

Inputs

Input Label
Input dataset Human_cRAP_Non_normal_transcripts_dB
Input dataset Fusion-database
Input dataset Input-RAW-FILE
Input dataset FragPipe_Experimental_design_tabular

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0 FASTA Merge Files and Filter Unique Sequences Merge_non-normal_fusion_FASTA-files
toolshed.g2.bx.psu.edu/repos/galaxyp/validate_fasta_database/validate_fasta_database/0.1.5 Validate FASTA Database Validation_of_Fasta_file
toolshed.g2.bx.psu.edu/repos/galaxyp/fragpipe/fragpipe/20.0+galaxy2 FragPipe - Academic Research and Education User License (Non-Commercial) Fragpipe
toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 Collapse Collection Extract_Peptides_from_Fragpipe
Grep1 Select Removing_known_human_peptides
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2 Query Tabular Extracting_Peptide-Candidates

Tools

Tool Links
Grep1
Remove beginning1
toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/fragpipe/fragpipe/20.0+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/validate_fasta_database/validate_fasta_database/0.1.5 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/nml/collapse_collections/collapse_dataset/5.1.0 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
  1. Click on 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 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:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
1 23219d5e3 2025-07-02 06:06:19 rename folders

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/neoantigen-fragpipe-discovery/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