diff --git a/R/flowr_local.R b/R/flowr_local.R
index 20bb509..35afcbe 100644
--- a/R/flowr_local.R
+++ b/R/flowr_local.R
@@ -55,11 +55,13 @@ install_node <- function(node_ver, verbose = FALSE, base_dir = get_default_node_
 #' @param flowr_ver The version of flowR to install.
 #' @param verbose Whether to print out information about the commands being executed.
 #' @param base_dir The base directory that Node was installed in, and where flowR should be installed. By default, this uses the package's installation directory through [get_default_node_base_dir()].
+#' @param std_out The std_out parameter passed to the sys call. See [sys::exec_background()] and [sys::exec_wait()] for more info.
+#' @param std_err The std_err parameter passed to the sys call. See [sys::exec_background()] and [sys::exec_wait()] for more info.
 #' @return The return value of the [exec_node_command()] call.
 #'
 #' @export
-install_flowr <- function(flowr_ver, verbose = FALSE, base_dir = get_default_node_base_dir()) {
-  exec_node_command("npm", c("install", "-g", paste0("--prefix=", get_node_exe_dir(base_dir)), paste0("@eagleoutice/flowr@", flowr_ver)), verbose, base_dir)
+install_flowr <- function(flowr_ver, verbose = FALSE, base_dir = get_default_node_base_dir(), std_out = TRUE, std_err = TRUE) {
+  exec_node_command("npm", c("install", "-g", paste0("--prefix=", get_node_exe_dir(base_dir)), paste0("@eagleoutice/flowr@", flowr_ver)), verbose, base_dir, FALSE, std_out, std_err)
 }
 
 #' Executes a local version of the flowR CLI with the given arguments in the given directory.
@@ -69,14 +71,16 @@ install_flowr <- function(flowr_ver, verbose = FALSE, base_dir = get_default_nod
 #' @param verbose Whether to print out information about the commands being executed.
 #' @param base_dir The base directory that Node and flowR were installed in. By default, this uses the package's installation directory through [get_default_node_base_dir()].
 #' @param background Whether the command should be executed as a background process.
+#' @param std_out The std_out parameter passed to the sys call. See [sys::exec_background()] and [sys::exec_wait()] for more info.
+#' @param std_err The std_err parameter passed to the sys call. See [sys::exec_background()] and [sys::exec_wait()] for more info.
 #' @return The return value of the [exec_node_command()] call, which is the exit code if background is false, or the pid if background is true.
 #'
 #' @export
-exec_flowr <- function(args, verbose = FALSE, base_dir = get_default_node_base_dir(), background = FALSE) {
+exec_flowr <- function(args, verbose = FALSE, base_dir = get_default_node_base_dir(), background = FALSE, std_out = TRUE, std_err = TRUE) {
   # we installed flowr globally (see above) in the scope of our local node installation, so we can find it here
   node_modules <- if (get_os() == "win") "node_modules" else file.path("lib", "node_modules")
   flowr_path <- file.path(get_node_exe_dir(base_dir), node_modules, "@eagleoutice", "flowr", "cli", "flowr.js")
-  exec_node_command("node", c(flowr_path, args), verbose, base_dir, background)
+  exec_node_command("node", c(flowr_path, args), verbose, base_dir, background, std_out, std_err)
 }
 
 #' Executes a local version of the flowR CLI with the given arguments in the given directory.
@@ -88,11 +92,13 @@ exec_flowr <- function(args, verbose = FALSE, base_dir = get_default_node_base_d
 #' @param verbose Whether to print out information about the commands being executed.
 #' @param cmd The command to use for docker. Defaults to "docker".
 #' @param background Whether the command should be executed as a background process.
+#' @param std_out The std_out parameter passed to the sys call. See [sys::exec_background()] and [sys::exec_wait()] for more info.
+#' @param std_err The std_err parameter passed to the sys call. See [sys::exec_background()] and [sys::exec_wait()] for more info.
 #' @return The return value of the [exec_node_command()] call, which is the exit code if background is false, or the pid if background is true.
 #'
 #' @export
-exec_flowr_docker <- function(docker_args, flowr_ver, flowr_args, verbose = FALSE, cmd = "docker", background = FALSE) {
-  exec_docker_command(c("run", "--rm", docker_args, paste0("eagleoutice/flowr:", flowr_ver), flowr_args), verbose, cmd, background)
+exec_flowr_docker <- function(docker_args, flowr_ver, flowr_args, verbose = FALSE, cmd = "docker", background = FALSE, std_out = TRUE, std_err = TRUE) {
+  exec_docker_command(c("run", "--rm", docker_args, paste0("eagleoutice/flowr:", flowr_ver), flowr_args), verbose, cmd, background, std_out, std_err)
 }
 
 #' Executes the given Node subcommand in the given arguments in the given directory.
@@ -103,10 +109,12 @@ exec_flowr_docker <- function(docker_args, flowr_ver, flowr_args, verbose = FALS
 #' @param verbose Whether to print out information about the commands being executed.
 #' @param base_dir The base directory that Node was installed in. By default, this uses the package's installation directory through [get_default_node_base_dir()].
 #' @param background Whether the command should be executed as a background process.
+#' @param std_out The std_out parameter passed to the sys call. See [sys::exec_background()] and [sys::exec_wait()] for more info.
+#' @param std_err The std_err parameter passed to the sys call. See [sys::exec_background()] and [sys::exec_wait()] for more info.
 #' @return The return value of the call, which is the exit code if background is false, or the pid if background is true.
 #'
 #' @export
-exec_node_command <- function(app = c("node", "npm", "npx"), args, verbose = FALSE, base_dir = get_default_node_base_dir(), background = FALSE) {
+exec_node_command <- function(app = c("node", "npm", "npx"), args, verbose = FALSE, base_dir = get_default_node_base_dir(), background = FALSE, std_out = TRUE, std_err = TRUE) {
   # linux/mac have binaries in the bin subdirectory, windows has node.exe and npm/npx.cmd in the root, bleh
   path <- if (get_os() == "win") paste0(app, if (app == "node") ".exe" else ".cmd") else file.path("bin", app)
   cmd <- file.path(get_node_exe_dir(base_dir), path)
@@ -114,9 +122,9 @@ exec_node_command <- function(app = c("node", "npm", "npx"), args, verbose = FAL
     print(paste0("Executing ", cmd, " ", paste0(args, collapse = " ")))
   }
   if (background) {
-    return(sys::exec_background(cmd, args))
+    return(sys::exec_background(cmd, args, std_out, std_err))
   } else {
-    return(sys::exec_wait(cmd, args))
+    return(sys::exec_wait(cmd, args, std_out, std_err))
   }
 }
 
@@ -127,17 +135,19 @@ exec_node_command <- function(app = c("node", "npm", "npx"), args, verbose = FAL
 #' @param verbose Whether to print out information about the commands being executed.
 #' @param cmd The command to use for docker. Defaults to "docker".
 #' @param background Whether the command should be executed as a background process.
+#' @param std_out The std_out parameter passed to the sys call. See [sys::exec_background()] and [sys::exec_wait()] for more info.
+#' @param std_err The std_err parameter passed to the sys call. See [sys::exec_background()] and [sys::exec_wait()] for more info.
 #' @return The return value of the call, which is the exit code if background is false, or the pid if background is true.
 #'
 #' @export
-exec_docker_command <- function(args, verbose = FALSE, cmd = "docker", background = FALSE) {
+exec_docker_command <- function(args, verbose = FALSE, cmd = "docker", background = FALSE, std_out = TRUE, std_err = TRUE) {
   if (verbose) {
     print(paste0("Executing ", cmd, " ", paste0(args, collapse = " ")))
   }
   if (background) {
-    return(sys::exec_background(cmd, args))
+    return(sys::exec_background(cmd, args, std_out, std_err))
   } else {
-    return(sys::exec_wait(cmd, args))
+    return(sys::exec_wait(cmd, args, std_out, std_err))
   }
 }
 
diff --git a/man/exec_docker_command.Rd b/man/exec_docker_command.Rd
index 8c8fddf..ee25c51 100644
--- a/man/exec_docker_command.Rd
+++ b/man/exec_docker_command.Rd
@@ -5,7 +5,14 @@
 \title{Executes the given docker command in the given directory.
 This function expects docker to exist on the system.}
 \usage{
-exec_docker_command(args, verbose = FALSE, cmd = "docker", background = FALSE)
+exec_docker_command(
+  args,
+  verbose = FALSE,
+  cmd = "docker",
+  background = FALSE,
+  std_out = TRUE,
+  std_err = TRUE
+)
 }
 \arguments{
 \item{args}{The arguments to pass to the docker command, as a character vector.}
@@ -15,6 +22,10 @@ exec_docker_command(args, verbose = FALSE, cmd = "docker", background = FALSE)
 \item{cmd}{The command to use for docker. Defaults to "docker".}
 
 \item{background}{Whether the command should be executed as a background process.}
+
+\item{std_out}{The std_out parameter passed to the sys call. See \code{\link[sys:exec]{sys::exec_background()}} and \code{\link[sys:exec]{sys::exec_wait()}} for more info.}
+
+\item{std_err}{The std_err parameter passed to the sys call. See \code{\link[sys:exec]{sys::exec_background()}} and \code{\link[sys:exec]{sys::exec_wait()}} for more info.}
 }
 \value{
 The return value of the call, which is the exit code if background is false, or the pid if background is true.
diff --git a/man/exec_flowr.Rd b/man/exec_flowr.Rd
index 5f90e24..908bce6 100644
--- a/man/exec_flowr.Rd
+++ b/man/exec_flowr.Rd
@@ -9,7 +9,9 @@ exec_flowr(
   args,
   verbose = FALSE,
   base_dir = get_default_node_base_dir(),
-  background = FALSE
+  background = FALSE,
+  std_out = TRUE,
+  std_err = TRUE
 )
 }
 \arguments{
@@ -20,6 +22,10 @@ exec_flowr(
 \item{base_dir}{The base directory that Node and flowR were installed in. By default, this uses the package's installation directory through \code{\link[=get_default_node_base_dir]{get_default_node_base_dir()}}.}
 
 \item{background}{Whether the command should be executed as a background process.}
+
+\item{std_out}{The std_out parameter passed to the sys call. See \code{\link[sys:exec]{sys::exec_background()}} and \code{\link[sys:exec]{sys::exec_wait()}} for more info.}
+
+\item{std_err}{The std_err parameter passed to the sys call. See \code{\link[sys:exec]{sys::exec_background()}} and \code{\link[sys:exec]{sys::exec_wait()}} for more info.}
 }
 \value{
 The return value of the \code{\link[=exec_node_command]{exec_node_command()}} call, which is the exit code if background is false, or the pid if background is true.
diff --git a/man/exec_flowr_docker.Rd b/man/exec_flowr_docker.Rd
index b85eac0..9031a7f 100644
--- a/man/exec_flowr_docker.Rd
+++ b/man/exec_flowr_docker.Rd
@@ -11,7 +11,9 @@ exec_flowr_docker(
   flowr_args,
   verbose = FALSE,
   cmd = "docker",
-  background = FALSE
+  background = FALSE,
+  std_out = TRUE,
+  std_err = TRUE
 )
 }
 \arguments{
@@ -26,6 +28,10 @@ exec_flowr_docker(
 \item{cmd}{The command to use for docker. Defaults to "docker".}
 
 \item{background}{Whether the command should be executed as a background process.}
+
+\item{std_out}{The std_out parameter passed to the sys call. See \code{\link[sys:exec]{sys::exec_background()}} and \code{\link[sys:exec]{sys::exec_wait()}} for more info.}
+
+\item{std_err}{The std_err parameter passed to the sys call. See \code{\link[sys:exec]{sys::exec_background()}} and \code{\link[sys:exec]{sys::exec_wait()}} for more info.}
 }
 \value{
 The return value of the \code{\link[=exec_node_command]{exec_node_command()}} call, which is the exit code if background is false, or the pid if background is true.
diff --git a/man/exec_node_command.Rd b/man/exec_node_command.Rd
index d4e7dff..15074f1 100644
--- a/man/exec_node_command.Rd
+++ b/man/exec_node_command.Rd
@@ -10,7 +10,9 @@ exec_node_command(
   args,
   verbose = FALSE,
   base_dir = get_default_node_base_dir(),
-  background = FALSE
+  background = FALSE,
+  std_out = TRUE,
+  std_err = TRUE
 )
 }
 \arguments{
@@ -23,6 +25,10 @@ exec_node_command(
 \item{base_dir}{The base directory that Node was installed in. By default, this uses the package's installation directory through \code{\link[=get_default_node_base_dir]{get_default_node_base_dir()}}.}
 
 \item{background}{Whether the command should be executed as a background process.}
+
+\item{std_out}{The std_out parameter passed to the sys call. See \code{\link[sys:exec]{sys::exec_background()}} and \code{\link[sys:exec]{sys::exec_wait()}} for more info.}
+
+\item{std_err}{The std_err parameter passed to the sys call. See \code{\link[sys:exec]{sys::exec_background()}} and \code{\link[sys:exec]{sys::exec_wait()}} for more info.}
 }
 \value{
 The return value of the call, which is the exit code if background is false, or the pid if background is true.
diff --git a/man/install_flowr.Rd b/man/install_flowr.Rd
index 57a4525..d5d735e 100644
--- a/man/install_flowr.Rd
+++ b/man/install_flowr.Rd
@@ -8,7 +8,9 @@ This function expects Node to have been installed using \code{\link[=install_nod
 install_flowr(
   flowr_ver,
   verbose = FALSE,
-  base_dir = get_default_node_base_dir()
+  base_dir = get_default_node_base_dir(),
+  std_out = TRUE,
+  std_err = TRUE
 )
 }
 \arguments{
@@ -17,6 +19,10 @@ install_flowr(
 \item{verbose}{Whether to print out information about the commands being executed.}
 
 \item{base_dir}{The base directory that Node was installed in, and where flowR should be installed. By default, this uses the package's installation directory through \code{\link[=get_default_node_base_dir]{get_default_node_base_dir()}}.}
+
+\item{std_out}{The std_out parameter passed to the sys call. See \code{\link[sys:exec]{sys::exec_background()}} and \code{\link[sys:exec]{sys::exec_wait()}} for more info.}
+
+\item{std_err}{The std_err parameter passed to the sys call. See \code{\link[sys:exec]{sys::exec_background()}} and \code{\link[sys:exec]{sys::exec_wait()}} for more info.}
 }
 \value{
 The return value of the \code{\link[=exec_node_command]{exec_node_command()}} call.