Pipelines: panoply_unified_workflow

panoply_unified_workflow

Description

Performs proteogenomic analysis on multiple omics types in parallel (ie panoply_main) and leverages additional analysis modules such as panoply_immune_analysis, panoply_blacksheep, and panoply_nmf.

This pipeline executes the following modules and pipelines:

• panoply_main
• panoply_immune_analysis
• panoply_immune_analysis_report
• panoply_blacksheep
• panoply_blacksheep_report
• panoply_nmf_workflow

Input

Required inputs:

• yaml: (.yaml file) parameters in yaml format
• job_id: (String) An identifier name given to the job
• run_ptmsea: please see run_ptmsea input parameter in panoply_main
• run_cmap: please see run_cmap input parameter in panoply_main
• run_mo_nmf: (String) true to run the panoply_nmf workflow on all omes combined or false to skip
• run_so_nmf: (String) true to run the panoply_nmf workflow on each ome independently or false to skip
• rna_data: (.gct file, default = this.rna_v3_ss) Input rna data matrix
• cna_data: (.gct file, default = this.cna_ss) Input cna data matrix

Optional inputs (at least one must be specified):

• prote_ome: (.gct file, default = this.proteome_ss) proteome data matrix
• phospho_ome: (.gct file, default = this.phosphoproteome_ss) phosphoproteome data matrix
• acetyl_ome: (.gct file, default = this.acetylome_ss) acetylome data matrix
• ubiquityl_ome: (.gct file, default = this.ubiquitylome_ss) ubiquitylome data matrix

Output

This pipeline outputs two .zip files:

1. all_results.zip This file contains complete results from all pipelines and modules run. The directory structure and results are formatted as follows:

• results:
  • proteogenomic_analysis: contains all results from panoply_main including a folder called all_html_reports which contains all reports produced from the panoply_main pipeline. If panoply_cmap_analysis was run, a folder named proteome_cmap_analysis will be present containing results from this module. Please see the outputs from panoply_main for more information.
  • blacksheep_outlier: contains a folder for each ome type it was run on. Each ome folder will contain panoply_blacksheep results. Please see the outputs from panoply_blacksheep for more information.
  • nmf: contains results from panoply_nmf
  • immune_analysis: contains results from panoply_immune_analysis

2. all_reports.zip This file contains all reports produced from every pipeline and module run. The directory structure for this file is formatted as follows:

• reports:
  • proteogenomic_analysis: contains all reports generated by the modules in panoply_main
  • blacksheep_outlier: contains all reports generated by panoply_blacksheep_report
  • nmf: contains all reports generated by panoply_nmf_report and panoply_ssgsea_report
  • immune_analysis: contains all reports produced by panoply_immune_analysis_report