Pipelines: panoply_main_internal

panoply_main_internal

Description

Performs single-omic analysis for a given -ome (e.g. proteome, transcriptomic, phosphoproteome, etc.). Use panoply_main to run this pipeline along with additional proteogenomic analyses, if RNA and CNA data are available.

This pipeline executes the following modules:

• panoply_association_workflow
• panoply_blacksheep_workflow
• panoply_ssgsea_workflow
• panoply_nmf_internal_workflow
• panoply_immune_analysis_workflow (transcriptomics only)
• single-sample PTM-SEA (phosphoproteome only)

Input

Required inputs:

• job_identifier: (String) An identifier name given to the job
• input_ome: (.gct file) Input ome data matrix
• sample_annotation: (File, default = this.annotation_ss) The annotation file for the given ome data
• 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).
• yaml: (.yaml file) parameters in yaml format

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_nmf: (String, default = true) true if nmf analysis is desired or false to skip

Optional inputs:

• sample_na_max: please see sample_na_max input parameter in panoply_association

• nmiss_factor: please see nmiss_factor input parameter in panoply_association

• duplicate_gene_policy: please see duplicate_gene_policy input parameter in panoply_harmonize

• gene_id_col: please see gene_id_col input parameter in panoply_harmonize

• standalone: (String, default = false) set to true to run as a self-contained module; when running panoply_main pipeline use false

• geneset_db: (String, default = this.gseaDB) please see gene_set_database input parameter in panoply_ssgsea

• ptm_db: (String, default = this.ptmseaDB) this is the gene_set_database for running ptmsea

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_association: please see groupsFile input parameter in panoply_association. Overrides default groups_file.
• groups_file_blacksheep: please see groupsFile input parameter in panoply_blacksheep. Overrides default groups_file.
• groups_file_immune: please see groupsFile input parameter in panoply_immune_analysis. Overrides default groups_file.
• groups_file_nmf: please see groups_file input parameter in panoply_nmf_postprocess. Overrides default groups_file.

Output

panoply_main_internal produces a tarfile and report file for each of its modules

• association_tar: tarfile output of panoply_association

• ssgsea_assoc_tars: ssGSEA results for all annotations analyzed in panoply_association

• association_report: report produced by panoply_association_report

• blacksheep_tar: tarfile output of panoply_blacksheep

• blacksheep_report: report produced by panoply_blacksheep_report

• ssgsea_ome_tar: tarfile output of panoply_ssgsea

• ssgsea_ome_report: report produced by panoply_ssgsea_report

• so_nmf_results: tarfile output of panoply_nmf, containing the results of NMF clustering

• so_nmf_figures: tarfile output of panoply_nmf_postprocess, containing various postprocessing and figures from NMF analysis

• so_nmf_report: report produced by panoply_nmf_report

• so_nmf_ssgsea_tar: ssGSEA results on the W-matrix from NMF results; GCT produced by panoply_nmf_postprocess

• so_nmf_ssgsea_report: report produced by panoply_ssgsea_report for NMF clustering results

• normalized_data_table.gct: normalized data matrix produced by panoply_normalize_ms_data

• immune_analysis_tar: tarfile output of panoply_immune_analysis, if applicable

• immune_report: report produced by panoply_immune_analysis_report, if applicable

• ptmsea_tar: tarfile output of PTM-SEA results produced by panoply_ssgsea, if applicable

• ptmsea_ome_report: report of PTM-SEA results produced by panoply_ssgsea_report, if applicable