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Pipelines: panoply_unified_workflow

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wcorinne edited this page Aug 29, 2025 · 7 revisions

panoply_unified_workflow

Description

Performs proteogenomic analysis on multiple omics types in parallel (ie panoply_main) and leverages additional analysis modules such as panoply_nmf, panoply_clumps_ptm_workflow, and panoply_metaboanalyst. It can optionally be used to normalize and filter -omic datasets using panoply_normalize_filter_workflow.

This pipeline executes the following modules and pipelines:

Input

Required inputs:

  • yaml: (.yaml file) parameters in yaml format
  • job_id: (String) An identifier name given to the job
  • groups_file: (File, default = this.groups_ss) The annotation file for the given ome data, subsetted to annotations of interest and used for analyses. Can be manually overriden for relevant modules (below).

-Omic Inputs

NOTE: 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
  • nglyco_ome: (.gct file, default = this.nglycoproteome_ss) nglycoproteome data matrix
  • methyl_ome: (.gct file, default = this.methylation_ss) methylation data matrix

Non-Proteomic Inputs

  • Genomic Inputs: must specify both RNA and CNA data, in order to run proteogenomic analyses in panoply_main
    • 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
  • metabol_ome: (.gct file, default = this.metabolome_ss) metabolome data matrix

Module Toggles:

  • run_ptmsea: (String, default = false) true if phosphoproteome data is being run and ptmsea analysis is desired or "false" to skip (this module takes additional time and higher cost to run)
  • run_clumps: (String, default = false) true if PTM data is being run and ClumpsPTM analysis is desired, or "false" to skip (this module takes additional time and higher cost to run)
  • run_cmap: (String, default = false) true if proteome data is being run and cmap analysis is desired or false to skip (this module takes additional time and higher cost to run)
  • run_nmf: (String, default = true) true if nmf analysis is desired or false to skip
  • run_omicsev: (String, default = true) true if OmicsEV analysis is desired or false to skip

Optional Inputs

Groups File Overrides

By default, all analyses take groups_file as the default annotations-file. However, for certain modules it may be desireable to exclude, add, or otherwise customize the annotations used. The following parameters allow groups-files to be overridden on a module-specific basis:

  • groups_file_clumpsptm: please see groupsFile input parameter in panoply_clumps_ptm_diffexp. Overrides default groups_file.
  • groups_file_metaboanlayst: please see groups_file input parameter in panoply_metaboanalyst. Overrides default groups_file.
  • groups_file_nmf: please see groups_file input parameter in panoply_nmf_postprocess. Overrides default groups_file.

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.
    • rna: contains all results from panoply_main_internal run on RNA data. Please see the outputs from panoply_main_internal for more information.
    • clumps_ptm: contains results from panoply_clumps_ptm_workflow, if applicable
    • metaboanalyst: contains results from panoply_metaboanalyst, if applicable
    • nmf: contains results from panoply_nmf
  1. 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:
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