Man pages for nf-osi/nfportalutils
NF Portal Utilities
| add_activity | Add activity to entity |
| add_activity_batch | Add activity to multiple entities |
| add_default_fileview | Create default project fileview |
| add_default_folders | Create default folders |
| add_default_wiki | Add default wiki |
| add_new_study_meta | Helpers —————-# Add meta for new studies as... |
| add_people_from_table | Update the People table from a source Table or View column |
| add_publication_from_pubmed | Add a publication to the publication table |
| add_publication_from_unpaywall | Add a publication or preprint to the publication table via... |
| add_publications_from_file | Add a batch of publications from spreadsheet |
| add_study_summary | Add studyId-summary key-value only |
| add_to_collection | Add to collection |
| add_to_scope | Add to scope |
| adjust_list_length | Adjust schema max list length based on hint |
| adjust_string_size | Adjust schema max size based on hint |
| adjust_view | Adjust view |
| annotate_aligned_reads | Annotate processed aligned reads |
| annotate_called_variants | Annotate somatic or germline variants output |
| annotate_cnv | Annotate CNV outputs from CNVKit |
| annotate_expression | Annotate processed expression output |
| annotate_reports_sarek | Annotate Sarek reports |
| annotate_with_manifest | Set annotations from a manifest |
| annotate_with_tool_stats | Make annotations from workflow tool stats |
| append_kv | Append key-value pair dependent on value being given |
| as_coll_items | Structure as collection items |
| as_mmd_link | Generate notation for mermaid.js link |
| as_mmd_node | Generate notation for mermaid.js nodes |
| assign_study_data_types | Summarize data types for the study |
| as_table_schema | Transform table data to target schema for Synapse storage |
| bad_url | Helper function to check urls |
| bare_syn_id | Extract synapse id from URI or other string |
| bipartite_mmd_template | Simple bipartite representation in mermaid charts |
| button_widget | Generate button widget for a Synapse wiki |
| byte_budget | Calculate byte budget for a schema |
| calc_study_dist_dtm | Calculate study distance based on summary text |
| calculate_related_studies | Calculate and add related studies to study table |
| cbp_add_clinical | Export and add clinical data to cBioPortal dataset |
| cbp_add_cna | Export and add CNA (seg) data to cBioPortal dataset |
| cbp_add_expression | Export and add expression data to cBioPortal dataset |
| cbp_add_maf | Export and add mutations data to cBioPortal dataset |
| cbp_datatypes | Enumerate combinations of valid cBP data types and data... |
| cbp_new_cancer_type | Create reference file for new cancer type |
| cbp_new_study | Initialize a new cBioPortal study dataset |
| check_access | Check access |
| check_byte_budget_col_swap | Check byte budget when swapping cols in schema |
| check_cbp_study_id | Check that in valid cBioPortal study dataset root |
| checked_message | Format checked message notification |
| check_readpair_validity | Check fastq read pair matches samplesheet read pair... |
| check_wiki_links | Check wiki links |
| cite_dataset | Generate example dataset citation |
| convert_to_stringlist | Convert a delimited string to a stringlist annotation |
| copy | Create copy of entity |
| copy_annotations | Copy annotations |
| data_curator_app_subpage | Create NF Data Curator App subpage |
| delete_provenance | Remove provenance info |
| derive_annotations | Derive annotations for processed output data |
| dot-add_publication_from_pubmed | Higher-level fun to generate 'add_publication_from_pubmed'... |
| dot-check_login | Checks .syn object exists. |
| dot-delim_string_to_vector | Convert a delimited string to vector, utility function. |
| dot-modify_annotation | Modify a single annotation on a single file |
| dot-replace_string_column_with_stringlist_column | Replace string column with stringlist column |
| dot-store_rows | Adds a row to a table. |
| dot-update_table_data | Replace/update table contents = input data must have ROW_ID... |
| dot-update_view_data | Replace/update table contents = input data must have ROW_ID,... |
| dsp_dataset_mapping | Wrapper to create Data Sharing Plan to project dataset... |
| dt_read | Download and read file to 'data.table' |
| find_child | Find id of a child entity in a container |
| find_child_type | Find children of type |
| find_data_root | Find data folder |
| find_in | Find in path |
| find_nf_asset | Find a standard nextflow workflow output asset |
| format_gene_expression_data | Format gene expression |
| from_pubmed | Get publication metadata from PubMed |
| gather_annotations | Internal helper for gathering annotations into a table using... |
| get_by_prop_from_json_schema | Look up connected nodes by specified property in JSON-LD... |
| get_cbio_filename | Get cBioPortal clinical file name based on clinical data type |
| get_dependency_from_json_schema | Get dependencies for node in JSON-LD schema |
| get_doi_meta | Get DOI metadata if it exists |
| get_project_wiki | Get wiki content of synapse project(s) |
| get_valid_values_from_json_schema | Retrieve valid subclasses of a value in a JSON-LD schema |
| grant_specific_file_access | Provide access to a specific set of files using a query... |
| identify_read_pair | Identify read pair from string |
| infer_data_type | Infer data type of a dataset folder |
| is_dataset | Check whether entity is dataset |
| is_dataset_collection | Check whether entity is dataset collection |
| is_file | Check whether entity is file |
| is_valid_syn_id | Validate a Synapse ID |
| is_valid_team | Check that is valid team in Synapse |
| is_valid_user | Check that is valid user in Synapse |
| key_label_to_id | Query for schema key id given label |
| latest_version | Get the latest version |
| list_project_datasets | List datasets in project |
| make_admin | Make a user or group full admin of a Synapse entity |
| make_cbio_clinical_header | Make header for cBioPortal clinical data file |
| make_folder | Create project folders |
| make_meta_clinical_generic | Generic template for clinical data file |
| make_meta_cna | Make meta file for cBioPortal copy number alteration data |
| make_meta_expression | Make meta file for cBioPortal expression data |
| make_meta_genomic_generic | Generic template for genomic-type data file |
| make_meta_maf | Make meta file for maf |
| make_meta_patient | Make patient meta file |
| make_meta_sample | Make sample meta file |
| make_meta_study_generic | Template for meta study file |
| make_public | Make public |
| make_public_viewable | Set public access to VIEW (READ) only for an entity |
| manifest_generate | Generate manifest via schematic service |
| manifest_passed | Provide a pass/fail summary result |
| manifest_validate | Validate manifest via schematic service |
| map_reports_sarek | Map out Sarek _report_ files |
| map_sample_input_ss | Parse nextflow samplesheet for sample inputs |
| map_sample_io | Map sample input-output |
| map_sample_output_rnaseq | Map sample to output from nf-rnaseq |
| map_sample_output_sarek | Map sample to output from nf-sarek |
| match_col | Find matching col in schema based on name |
| meta_qc_dataset | QC dataset metadata with pass/fail result |
| meta_qc_project | QC metadata at the project level with pass/fail result |
| missing_annotation_email | Convert a delimited string to a stringlist annotation |
| new_col | Create new col |
| new_dataset | Create new dataset with given items |
| new_project | Create a new project |
| new_project_strict | Create a strictly new project |
| new_view | Create a view |
| nf_cnv_dataset | Create dataset for CNVKit results |
| nf_sarek_datasets | Create datasets for Sarek-called somatic or germline variants... |
| nf_star_salmon_datasets | Create dataset for STAR-Salmon expression quantification... |
| nf_workflow_version | Return workflow version according to workflow meta |
| pipe | Pipe operator |
| ppp_mmd_template | Pretty processing provenance mermaid template for the portal |
| precheck_manifest | Precheck a manifest |
| processing_flowchart | Wrapper to create data-driven flowchart with pretty... |
| register_study | Register a NEW project for the NF Data Portal in *Portal -... |
| register_study_files | Register a project's files in *Portal - Files* |
| remanifest | Reconstitute a manifest |
| remove_button | Remove button from a project wiki |
| remove_wiki_subpage | Remove a subpage from a project wiki |
| save_manifest | Save manifest |
| schema_max_str_len | Consult schema about max string length |
| strlist_JSON | Convert delimited record to JSON representation needed by a... |
| summarize_attribute | Helper summarization util |
| summarize_file_access | Summarize file access for files within some view |
| swap_col | Swap out old column for a new column in a schema |
| syn_login | Logs into Synapse. |
| table_query | Generic table query |
| tersely | Terse error messages please |
| test_failed | Format a test fail message. |
| test_passed | Format a test passed message. |
| update_items | Apply updates to current collection of items |
| update_study_annotations | Updates a set of files with project-level annotations. |
| use_latest_in_collection | Update item versions to "latest" in a collection |
| use_ref_map | Read and use a mapping file |
| walk | Walk through a directory |
| which_coll_type | Which collection type |
| wiki_mod | Add markup to a project wiki |
| write_cbio_clinical | Write cBioPortal clinical file |
| write_meta | Write meta file |
