GigaScience_Peptide_Annotation_demonstration_STS26T_neoantigen_candidates_workflow
1.0

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Workflow Type: Galaxy

Annotating the novel peptides

Associated Tutorial

This workflows is part of the tutorial Neoantigen 4: Variant Annotation, available in the GTN

Features

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, Saskia Hiltemann, Katherine Do

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SEEK ID: https://workflowhub.eu/workflows/1790?version=1

Inputs

ID Name Description Type
Annotated-GffCompared-GTFtoBED #main/Annotated-GffCompared-GTFtoBED Annotated GffCompared GTF to BED
  • File
Fragpipe-Peptide-Report #main/Fragpipe-Peptide-Report Peptide report from Fragpipe workflow
  • File
Homo_sapiens.GRCh38_canon.106.gtf #main/Homo_sapiens.GRCh38_canon.106.gtf Homo_sapiens.GRCh38_canon.106.gtf
  • File
Novel_Peptides #main/Novel_Peptides Candidate Neoantigens from Fragpipe Workflow
  • File

Steps

ID Name Description
4 Peptide_to_Protein_Annotation Extracting the information from Fragpipe for the Novel peptides toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2
5 FASTA-IEDB FASTA file for IEDB toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1
6 Converting_pipes_to_columns converting pipes to columns Convert characters1
7 Modifying-string-name Modifying-string-name toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3
8 Converting_colons_to_columns converting colons to columns Convert characters1
9 Extracting-info-from-GFFtobed Extracting-info-from-GFFtobed toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2
10 Table-processing-3 multiplying start and stop of the peptide location with 3 to calculate genomic coordinates toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2
11 Peptide-location-generation calculation genomic coordinates looking at peptide location toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2
12 BED-File-for-PepPointer Extracting bed file for Peppointer toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2
13 PepPointer PepPointer to add annotation to the peptides at Genomic level toolshed.g2.bx.psu.edu/repos/galaxyp/pep_pointer/pep_pointer/0.1.3+galaxy1
14 Summary-Neoantigen Summary file for Neoantigen toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2

Outputs

ID Name Description Type
BED-File-for-PepPointer #main/BED-File-for-PepPointer n/a
  • File
Extracting-info-from-GFFtobed #main/Extracting-info-from-GFFtobed n/a
  • File
FASTA-IEDB #main/FASTA-IEDB n/a
  • File
Modified-string-name #main/Modified-string-name n/a
  • File
Neoantigen_summary #main/Neoantigen_summary n/a
  • File
PepPointer-Annotated-Peptides #main/PepPointer-Annotated-Peptides n/a
  • File
Peptide-location-generation #main/Peptide-location-generation n/a
  • File
Peptide_to_Protein_Annotation #main/Peptide_to_Protein_Annotation n/a
  • File
Table-processing-1 #main/Table-processing-1 n/a
  • File
Table-processing-2 #main/Table-processing-2 n/a
  • File
Table-processing-3 #main/Table-processing-3 n/a
  • File

Version History

1.0 (earliest) Created 7th Jul 2025 at 14:15 by GTN Bot

Added/updated 4 files


Open master 5898e69
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Views: 812   Downloads: 149   Runs: 0

Created: 7th Jul 2025 at 14:15

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Total size: 207 KB
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