Address CMD check doc complaints, update NAMESPACE and bump pkg version

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: nfportalutils
 Title: NF Portal Utilities
-Version: 0.0.0.9210
+Version: 0.0.0.9300
 Authors@R: c(
     person(given = "Robert", family = "Allaway", role = c("aut", "cre"),
            email = "[email protected]",

NAMESPACE

@@ -16,6 +16,7 @@ export(add_people_from_table)
 export(add_publication_from_pubmed)
 export(add_publication_from_unpaywall)
 export(add_publications_from_file)
+export(add_to_collection)
 export(annotate_aligned_reads)
 export(annotate_called_variants)
 export(annotate_expression)
@@ -49,7 +50,10 @@ export(map_sample_io)
 export(map_sample_output_rnaseq)
 export(map_sample_output_sarek)
 export(missing_annotation_email)
+export(new_dataset)
 export(new_project)
+export(nf_sarek_datasets)
+export(nf_star_salmon_datasets)
 export(processing_flowchart)
 export(qc_manifest)
 export(register_study)
@@ -61,6 +65,7 @@ export(syn_login)
 export(syncBP_maf)
 export(table_query)
 export(update_study_annotations)
+export(use_latest_in_collection)
 export(wiki_mod)
 import(data.table)
 import(reticulate)

R/datasets.R

@@ -52,7 +52,7 @@ update_items <- function(current_coll, update_coll) {
 #' Update an _existing_ collection so that all items or a subset of items reference their latest version.
 #' This should work for both datasets (collection of files) and dataset collections (collection of datasets).
 #' 
-#' @param collection_id 
+#' @param collection_id Collection id.
 #' @param items Vector of dataset ids for which to update reference to latest version, 
 #' or "all" (default) to update all in the dataset collection.
 #' @export
@@ -93,7 +93,7 @@ use_latest_in_collection <- function(collection_id, items = "all") {
 #' Thus, while this is generic enough to handle both datasets and dataset collections 
 #' it is expected to be used more for dataset collections given that the dataset method is provided.
 #' 
-#' @param collection_id Id of the collection.
+#' @param collection_id Collection id.
 #' @param items Character vector of one or more dataset entity ids to add.
 #' @param check_items Whether to check that ids are really appropriate item types and remove non-appropriate item types
 #' to help avoid Synapse errors (default `FALSE` because in most cases `items` are curated, and using check will be slower).
@@ -171,6 +171,7 @@ new_dataset <- function(name, parent, items, item_version = NULL, dry_run = TRUE
 #' 
 #' @inheritParams new_dataset
 #' @param output_map The `data.table` returned from `map_sample_output_sarek`. See details for alternatives.
+#' @param workflow One of workflows used.
 #' @param verbose Optional, whether to be verbose -- defaults to TRUE.
 #' @import data.table
 #' @return A list of dataset objects.