GigaScience_Database_merge_FragPipe_STS26T_demonstration
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Workflow Type: Galaxy

Merging 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

Workflow Author(s): GalaxyP

Tutorial Author(s): Subina Mehta, Katherine Do, James Johnson

Tutorial Contributor(s): Pratik Jagtap, Timothy J. Griffin

SEEK ID: https://dev.workflowhub.eu/workflows/1384?version=1

ID	Name	Description	Type
FragPipe_Experimental_design_tabular	#main/FragPipe_Experimental_design_tabular	Design file	File
Fusion-database	#main/Fusion-database	Arriba Fusion db	File
Human_cRAP_Non_normal_transcripts_dB	#main/Human_cRAP_Non_normal_transcripts_dB	Non-Normal databases i.e CustomProDB and StringTie	File
Input-RAW-FILE	#main/Input-RAW-FILE	Input RAW file	File

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_NeoAntigen_Peptides_for_PepQuery	extracts those peptides with no gene annotation and mapped genes toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2

ID	Name	Description	Type
Fragpipe-Peptide-Report	#main/Fragpipe-Peptide-Report	n/a	File
Fragpipe_output_peptide	#main/Fragpipe_output_peptide	n/a	File
Fragpipe_output_protein	#main/Fragpipe_output_protein	n/a	File
Fragpipe_output_psm	#main/Fragpipe_output_psm	n/a	File
Neoantigen_Peptide_Candidates_for_PepQuery	#main/Neoantigen_Peptide_Candidates_for_PepQuery	n/a	File
Non_normal_and_Fusion_dB	#main/Non_normal_and_Fusion_dB	n/a	File
Removing_known_human_peptides_and_contaminants	#main/Removing_known_human_peptides_and_contaminants	n/a	File
Validated-fasta	#main/Validated-fasta	n/a	File

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Created: 20th Jan 2025 at 13:07