_pkgdown.yml

url: ~
template:
  bootstrap: 5

reference:
- title: Table Utils
- subtitle: Main PORTAL table data update and management
  desc: Augment and update one of the main portal tables (e.g. Portal - Studies)
- contents:
  - starts_with("add_publication")
  - assign_study_data_types
  - calculate_related_studies
  - register_study
  - add_people_from_table
  - register_study_files
  - summarize_attribute
- subtitle: Lower-level table maintenance
- contents:
  - adjust_view
  - swap_col
  - byte_budget

- title: Project Configuration and Management
  desc: Create or retrofit an NF project to expected default structure and assets
- contents:
  - new_project
  - add_default_fileview
  - add_default_folders
  - make_admin

- title: Metadata Utils
- subtitle: General annotations
  desc: Add and manage annotations on Synapse entities
- contents:
  - update_study_annotations
  - annotate_with_manifest
  - copy_annotations
  - .modify_annotation
  - meta_qc_dataset
  - meta_qc_project
  - manifest_generate
  - manifest_validate
  - manifest_passed
  - precheck_manifest
  - remanifest
  - infer_data_type
- subtitle: Special annotation of nextflow processed data
  desc: Special annotation of nextflow processed data
- contents:
  - map_reports_sarek
  - map_sample_input_ss
  - map_sample_io
  - map_sample_output_rnaseq
  - map_sample_output_sarek
  - annotate_aligned_reads
  - annotate_called_variants
  - annotate_expression
  - annotate_cnv
  - annotate_reports_sarek
  - annotate_with_tool_stats
  - nf_workflow_version

- title: Dataset Creation and Management
- subtitle: General dataset creation and citation
  desc: Create datasets in general
- contents:
  - new_dataset
- subtitle: Specialized dataset creation
  desc: Create specialized datasets for nextflow processed data, i.e. with some custom construction queries and title templating.
- contents:
  - nf_sarek_datasets
  - nf_star_salmon_datasets
  - nf_cnv_dataset
- subtitle: Working with dataset collections to manage datasets after creation
- contents:
  - add_to_collection
  - use_latest_in_collection
  - update_items

- title: Data Model Utils
  desc: Talk to a JSON-LD data model important to the portal data (i.e. NF-metadata-dictionary)
- contents:
  - get_by_prop_from_json_schema
  - get_dependency_from_json_schema
  - get_valid_values_from_json_schema
  - key_label_to_id
  - schema_max_str_len

- title: Governance Utils
  desc: Analyze and manage data access/restrictions
- contents:
  - make_public_viewable
  - make_public
  - check_access
  - summarize_file_access
  - grant_specific_file_access

- title: Search Utils
  desc: Help locate Synapse accessions, etc.
- contents:
  - contains("find")

- title: Provenance Utils
  desc: Manage provenance metadata
- contents:
  - contains("activity")
  - delete_provenance

- title: Content Utils
  desc: Create and manage content for projects and pages
- contents:
  - add_default_wiki
  - wiki_mod
  - remove_wiki_subpage
  - data_curator_app_subpage
  - get_project_wiki
  - check_wiki_links
  - remove_button
- subtitle: Figures and diagrams
  desc: Supplemental figures and diagrams that go into Wikis or other places
- contents:
  - processing_flowchart
  - dsp_dataset_mapping
  - bipartite_mmd_template

- title: Export Data to Other Platforms
  desc: Helpers to export/release NF data to other platforms/databases.
- subtitle: cBioPortal
  desc: Export data as a cBioPortal study
- contents:
  - cbp_new_study
  - cbp_new_cancer_type
  - cbp_add_maf
  - cbp_add_clinical
  - cbp_add_expression
  - cbp_add_cna

- title: Quality Control and Testing Utils
  desc: QC data
- contents:
  - check_readpair_validity
  - identify_read_pair
  - test_failed
  - test_passed

- title: Basic Utils
  desc: Low-level functions
- contents:
  - syn_login
  - table_query
  - as_table_schema
  - make_folder
  - add_to_scope
  - new_view
  - list_project_datasets
  - latest_version
  - walk
  - copy
  - convert_to_stringlist
  - bare_syn_id
  - bad_url
  - .update_table_data
  - .update_view_data
  - from_pubmed

- title: Internal/experimental
  description: Mostly meant to be internal or experimental stuff
- contents:
  - .delim_string_to_vector
  - .replace_string_column_with_stringlist_column
  - .store_rows
  - missing_annotation_email
  - get_doi_meta
  - cite_dataset