GigaScience_Database_merge_FragPipe_STS26T_demonstration 2.0
Visit source
Download RO-Crate
Run on GalaxyMerging Fusion and non-normal databases + Discovery peptidomics using FragPipe
Associated Tutorial
This workflows is part of the tutorial Neoantigen 3: Database merge and FragPipe discovery, available in the GTN
Features
- Includes a Galaxy Workflow Report
Thanks to...
Workflow Author(s): GalaxyP
Tutorial Author(s): Subina Mehta, Katherine Do, James Johnson
Tutorial Contributor(s): Pratik Jagtap, Timothy J. Griffin, Subina Mehta
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| FragPipe_Experimental_design_tabular | #main/FragPipe_Experimental_design_tabular | Design file |
|
| Fusion-database | #main/Fusion-database | Arriba Fusion db |
|
| Human_cRAP_Non_normal_transcripts_dB | #main/Human_cRAP_Non_normal_transcripts_dB | Non-Normal databases i.e CustomProDB and StringTie |
|
| Input-RAW-FILE | #main/Input-RAW-FILE | Input RAW file |
|
Steps
| ID | Name | Description |
|---|---|---|
| 4 | Merge_non-normal_fusion_FASTA-files | combine Fusion and Non Normal databases toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0 |
| 5 | Validation_of_Fasta_file | Take the Passed fasta file toolshed.g2.bx.psu.edu/repos/galaxyp/validate_fasta_database/validate_fasta_database/0.1.5 |
| 6 | Fragpipe | Non tryptic fragpipe toolshed.g2.bx.psu.edu/repos/galaxyp/fragpipe/fragpipe/20.0+galaxy2 |
| 7 | Extract_Peptides_from_Fragpipe | collapse peptide report toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
| 8 | Removing_known_human_peptides | removing anything that matches _HUMAN Grep1 |
| 9 | Extracting_Peptide-Candidates | toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2 |
| 10 | Neoantigen_Peptide_Candidates_for_PepQuery | Remove beginning1 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Extracting_Peptide-Candidates | #main/Extracting_Peptide-Candidates | n/a |
|
| Fragpipe-Peptide-Report | #main/Fragpipe-Peptide-Report | n/a |
|
| Fragpipe_output_peptide | #main/Fragpipe_output_peptide | n/a |
|
| Fragpipe_output_protein | #main/Fragpipe_output_protein | n/a |
|
| Fragpipe_output_psm | #main/Fragpipe_output_psm | n/a |
|
| Non_normal_and_Fusion_dB | #main/Non_normal_and_Fusion_dB | n/a |
|
| Removing_known_human_peptides | #main/Removing_known_human_peptides | n/a |
|
| Validated-fasta | #main/Validated-fasta | n/a |
|
Version History
master
Creators and Submitter
Views: 1234 Downloads: 172 Runs: 0
Created: 2nd Jun 2025 at 10:52
Tags AttributionsNone
Related items
Teams: Galaxy Training Network
Organizations: Galaxy
I'm a bot managed by @hexylena to upload workflows from the Galaxy Training Network to the WorkflowHub. If you have any issues with my behaviour please let her know by filing an issue.
Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.
- Accessible: Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface.
- Reproducible: Galaxy captures all the metadata from an analysis, making it completely reproducible.
- Transparent: Users share and publish analyses via interactive pages that can enhance analyses with user annotations.
- Scalable: Galaxy can run ...
Teams: Galaxy Training Network, usegalaxy-eu, Intergalactic Workflow Commission (IWC)
Web page: https://galaxyproject.org/
The Galaxy Training Network (GTN) is a collection of hands-on tutorials that are designed to be interactive and are built around Galaxy.
These tutorials can be used for learning and teaching how to use Galaxy for general data analysis, as well as a wide array of hands-on tutorials covering specific domains such as assembly, RNA-Seq analysis, deep learning, climate analysis, and more!
