diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown.yml.txt
similarity index 100%
rename from .github/workflows/pkgdown.yml
rename to .github/workflows/pkgdown.yml.txt
diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml.txt
similarity index 100%
rename from .github/workflows/pre-commit.yml
rename to .github/workflows/pre-commit.yml.txt
diff --git a/R/personalis.R b/R/personalis.R
index a5d25b8..59b3a46 100644
--- a/R/personalis.R
+++ b/R/personalis.R
@@ -52,7 +52,7 @@ read_personalis <- function(pathlist) {
 #
 
 #' Read in gene expression data from personalis folders
-#' @param sample_list A vector of paths to personalis folders
+#' @param sample_paths A vector of paths to personalis folders
 #' @return SummarizedExperiment
 #' @export
 read_personalis_gene_expression <- function(sample_paths) {
@@ -95,8 +95,28 @@ read_personalis_gene_expression_sample <- function(sample_folder) {
 # -------------------- SMALL VARIANTS --------------------
 #
 
-#' Read in small variant data from personalis folders
+#' Read in small variant data from personalis folder
+#' We only read in the "Preferred Transcript" report here:
+#'
+#' Preferred Transcript: The RefSeq accession.version for the transcript used for variant analysis.
+#' Personalis uses a curated list of transcripts, which is based on the number of
+#' times a transcript (accession.version) is referred to in COSMIC. If not present in
+#' COSMIC, the default transcript would be the one corresponding to the longest CDS.
+#' (source: Personalis Analysis_Pipeline_Documentation)
+#'
+#' We also do not read the `cancer_clinical_research`, the `cancer_research` and the `lowpupulationfreq` reports,
+#' because they are subsets of the full report.
+#'
+#' In addition, Personalis also provides raw VCF files with all (unfiltered) variants. We currently don't
+#' read them in because without additional filtering they are not very useful. If you need this level of information,
+#' feel free to start from the raw vcf files or even run your own variant calling based on the FASTQ files.
+#'
 #' @param sample_paths A vector of paths to personalis folders
+#' @param sample_type Can be one or multiple of of 'tumor', 'normal', or 'somatic'.
+#'   'tumor' refers to tumor sample vs. genome reference (i.e. somatic+germline mutations),
+#'   'normal' refers to normal sample vs. genome reference (i.e. germline mutations) and
+#'   'somatic' refers to tumor vs. normal (i.e. somatic mutations only).
+#' @param modality modality from which the variants were called. Can be either 'DNA' or 'RNA'
 #' @return SummarizedExperiment
 #' @importFrom dplyr select
 #' @importFrom purrr map
@@ -252,6 +272,7 @@ read_personalis_somatic_variants_summary_statistics <- function(sample_folder, m
 
 #' Read Personalis CNV data for a list of samples
 #' @return SummarizedExperiment
+#' @param sample_paths List of directories with Personalis samples
 #' @importFrom purrr map
 #' @export
 read_personalis_cnv_reports <- function(sample_paths) {
diff --git a/man/read_personalis_cnv_reports.Rd b/man/read_personalis_cnv_reports.Rd
index c615234..5d48637 100644
--- a/man/read_personalis_cnv_reports.Rd
+++ b/man/read_personalis_cnv_reports.Rd
@@ -6,6 +6,9 @@
 \usage{
 read_personalis_cnv_reports(sample_paths)
 }
+\arguments{
+\item{sample_paths}{List of directories with Personalis samples}
+}
 \value{
 SummarizedExperiment
 }
diff --git a/man/read_personalis_gene_expression.Rd b/man/read_personalis_gene_expression.Rd
index 0f57891..389a8a1 100644
--- a/man/read_personalis_gene_expression.Rd
+++ b/man/read_personalis_gene_expression.Rd
@@ -7,7 +7,7 @@
 read_personalis_gene_expression(sample_paths)
 }
 \arguments{
-\item{sample_list}{A vector of paths to personalis folders}
+\item{sample_paths}{A vector of paths to personalis folders}
 }
 \value{
 SummarizedExperiment
diff --git a/man/read_personalis_small_variant_reports.Rd b/man/read_personalis_small_variant_reports.Rd
index 298aa55..085c7e2 100644
--- a/man/read_personalis_small_variant_reports.Rd
+++ b/man/read_personalis_small_variant_reports.Rd
@@ -2,16 +2,36 @@
 % Please edit documentation in R/personalis.R
 \name{read_personalis_small_variant_reports}
 \alias{read_personalis_small_variant_reports}
-\title{Read in small variant data from personalis folders}
+\title{Read in small variant data from personalis folder
+We only read in the "Preferred Transcript" report here:}
 \usage{
 read_personalis_small_variant_reports(sample_paths, modality, sample_type)
 }
 \arguments{
 \item{sample_paths}{A vector of paths to personalis folders}
+
+\item{modality}{modality from which the variants were called. Can be either 'DNA' or 'RNA'}
+
+\item{sample_types}{Can be ome or multiple of of 'tumor', 'normal', or 'somatic'.
+'tumor' refers to tumor sample vs. genome reference (i.e. somatic+germline mutations),
+'normal' refers to normal sample vs. genome reference (i.e. germline mutations) and
+'somatic' refers to tumor vs. normal (i.e. somatic mutations only).}
 }
 \value{
 SummarizedExperiment
 }
 \description{
-Read in small variant data from personalis folders
+Preferred Transcript: The RefSeq accession.version for the transcript used for variant analysis.
+Personalis uses a curated list of transcripts, which is based on the number of
+times a transcript (accession.version) is referred to in COSMIC. If not present in
+COSMIC, the default transcript would be the one corresponding to the longest CDS.
+(source: Personalis Analysis_Pipeline_Documentation)
+}
+\details{
+We also do not read the \code{cancer_clinical_research}, the \code{cancer_research} and the \code{lowpupulationfreq} reports,
+because they are subsets of the full report.
+
+In addition, Personalis also provides raw VCF files with all (unfiltered) variants. We currently don't
+read them in because without additional filtering they are not very useful. If you need this level of information,
+feel free to start from the raw vcf files or even run your own variant calling based on the FASTQ files.
 }