GigaScience_Database_merge_FragPipe_STS26T_demonstration

proteomics-neoantigen-3-fragpipe-discovery/main-workflow

Author(s)
GalaxyP
version Version
1
last_modification Last updated
Jan 14, 2025
license License
CC-BY-4.0
galaxy-tags Tags
name:neoantigen

Features
Tutorial
hands_on Neoantigen 3: Database merge and FragPipe discovery

Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:
RO-Crate logo with flask Download Workflow RO-Crate
Launch in Tutorial Mode question
galaxy-download 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;
  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;
  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;
  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;
  190bb3e5-3359-4ac3-9515-055fe73926da["Output\nRemoving_known_human_peptides_and_contaminants"];
  8 --> 190bb3e5-3359-4ac3-9515-055fe73926da;
  style 190bb3e5-3359-4ac3-9515-055fe73926da stroke:#2c3143,stroke-width:4px;
  9["Extracting_NeoAntigen_Peptides_for_PepQuery"];
  8 -->|out_file1| 9;
  848d90aa-2d7e-4a96-8918-57efa8705dc1["Output\nNeoantigen_Peptide_Candidates_for_PepQuery"];
  9 --> 848d90aa-2d7e-4a96-8918-57efa8705dc1;
  style 848d90aa-2d7e-4a96-8918-57efa8705dc1 stroke:#2c3143,stroke-width:4px;

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_NeoAntigen_Peptides_for_PepQuery

Tools

Tool Links
Grep1
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
  • 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:

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-3-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