Support Modules: panoply_download

panoply_download

Description

Assembles the outputs from various analysis and report modules in the panoply_main pipeline into a coherent directory structure and creates two final output tarballs containing: (i) reports and relevant output tables/plots for all analysis modules and (ii) the complete results from the entire pipeline.

Input

Required inputs:

• analysisDir: (String) name of analysis directory

• output_prefix: (String) prefix added to the summary_tar and full_tar output names (usually set to omics type eg: 'proteome' etc.)

• association_tar: (.tar file) results from panoply_association

• blacksheep_tar: (.tar file) tarball from blacksheep outlier analysis

• ssgsea_assoc_tars: (Array[File]) array of .tar files from ssGSEA results from panoply_association

• ssgsea_ome_tar: (.tar file) single-sample GSEA results of panoply_ssgsea

Optional inputs:

• summary_tar: (String, default = 'panoply_main_summary.tar') name of output summary .tar file
• full_tar: (String, default = 'panoply_main_full.tar') name of output full .tar file
• ssgsea_assoc_dir: (String, default = 'ssgsea_assoc') directory containing ssGSEA Association results

Optional Analysis Modules

• cna_corr_tar: (.tar file) tarball containing all proteogenomic analysis results from panoply_main
• so_nmf_results: (.tar file) tarball from single-omic nmf clustering
• so_nmf_figures: (.tar file) tarball with figures from nmf postprocessing
• so_nmf_ssgsea_tar: (.tar file) tarball with ssgsea results on the W-Matrix from single-omic NMF clustering

Optional QC Modules

• omicsev_tar: (.tar file) results from panoply_omicsev
• cosmo_tar: (.tar file) results from panoply_cosmo

-ome Specific Modules

• immune_analysis_tar: (File) RNA-only; immune analysis results from panoply_immune_analysis_workflow
• ptmsea: (File) phosphoproteome-only; PTM-SEA results from panoply_ssgsea

Output

• summary: Summary .tar file
• full: Full .tar file