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Customizing PANOPLY
PANOPLY can be customized using the flexibility and customization abilities of Terra. [Terra Support] (https://support.terra.bio/) includes documentation, tutorials and guides to help users add new tasks and customize workflows. Customizing PANOPLY will require some programming ability and comfort with command-line environments. Here, we present links to Terra support/documentation to point users to the appropriate resources.
PANOPLY workflows can be customized by (i) adding/removing tasks from existing workflows or (ii) creating new workflows combining existing tasks in different ways. The following provide pointers to how tasks and workflows are structured.
Users can add new algorithms to PANOPLY by encapsulating them into a docker, and then using these dockers in tasks and workflows.
Users can explore the hydrant and src subdirectories in the PANOPLY repository to see examples of how docker images are created for R code, how these images are converted to tasks using WDL, and how multiple tasks are strung together into a full pipeline using WDL workflows.
- Home
- PANOPLY Tutorial
- Data Preparation Modules
- Data Analysis Modules
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Report Modules
- panoply_association_report
- panoply_blacksheep_report
- panoply_cna_correlation_report
- panoply_cons_clust_report
- panoply_immune_analysis_report
- panoply_mimp_report
- panoply_nmf_report
- panoply_normalize_ms_data_report
- panoply_rna_protein_correlation_report
- panoply_sampleqc_report
- panoply_sankey_report
- panoply_ssgsea_report
- Support Modules
- Navigating Results
- PANOPLY without Terra
- Customizing PANOPLY
- Pipelines