diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
index e3521739c2..5068b961f7 100644
--- a/.github/CODEOWNERS
+++ b/.github/CODEOWNERS
@@ -208,3 +208,6 @@ ush/python/pygfs/ufswm/gfs.py @aerorahul
 ush/python/pygfs/ufswm/ufs.py @aerorahul
 ush/python/pygfs/utils/__init__.py @aerorahul
 ush/python/pygfs/utils/marine_da_utils.py @guillaumevernieres @AndrewEichmann-NOAA
+
+# Specific workflow scripts
+workflow/generate_workflows.sh @DavidHuber-NOAA
diff --git a/workflow/generate_workflows.sh b/workflow/generate_workflows.sh
new file mode 100755
index 0000000000..ab40214655
--- /dev/null
+++ b/workflow/generate_workflows.sh
@@ -0,0 +1,532 @@
+#!/usr/bin/env bash
+
+###
+function _usage() {
+   cat <<-EOF
+   This script automates the experiment setup process for the global workflow.
+   Options are also available to update submodules, build the workflow (with
+   specific build flags), specicy which YAMLs and YAML directory to run, and
+   whether to automatically update your crontab.
+
+   Usage: generate_workflows.sh [OPTIONS] /path/to/RUNTESTS
+          or
+          RUNTESTS=/path/to/RUNTESTS generate_workflows.sh [OPTIONS]
+
+    -H Root directory of the global workflow.
+       If not specified, then the directory is assumed to be one parent
+       directory up from this script's residing directory.
+
+    -b Run build_all.sh with default flags
+       (build the UFS, UPP, UFS_Utils, and GFS-utils only
+
+    -B "build flags"
+       Run build_all.sh with the build specified flags.  Refer to
+       build_all.sh -h for a list of valid flags.
+       NOTE: the list of build flags MUST be in quotes.
+
+    -u Update submodules before building and/or generating experiments.
+
+    -y "list of YAMLs to run"
+       If this option is not specified, the default case (C48_ATM) will be
+       run.  This option is overidden by -G or -E (see below).
+       Example: -y "C48_ATM C48_S2SW C96C48_hybatmDA"
+
+    -Y /path/to/directory/with/YAMLs
+       If this option is not specified, then the \${HOMEgfs}/ci/cases/pr
+       directory is used.
+
+    -G Run all valid GFS cases in the specified YAML directory.
+       If -b is specified, then "-g -u" (build the GSI and GDASApp)
+       will be passed to build_all.sh unless -B is also specified.
+       Note that these builds are disabled on some systems, which
+       will result in a warning from build_all.sh.
+
+    -E Run all valid GEFS cases in the specified YAML directory.
+       If -b is specified, then "-w" will be passed to build_all.sh
+          unless -B is also specified.
+
+    -S (Not yet supported!)
+       Run all valid SFS cases in the specified YAML directory.
+
+    NOTES:
+         - Only one of -G -E or -S may be specified
+         - Valid cases are determined by the experiment:system key as
+           well as the skip_ci_on_hosts list in each YAML.
+
+    -A "HPC account name"  Set the HPC account name.
+       If this is not set, the default in
+       \$HOMEgfs/ci/platform/config.\$machine
+       will be used.
+
+    -c Append the chosen set of tests to your existing crontab
+       If this option is not chosen, the new entries that would have been
+       written to your crontab will be printed to stdout.
+       NOTES:
+          - This option is not supported on Gaea.  Instead, the output will
+            need to be written to scrontab manually.
+          - For Orion/Hercules, this option will not work unless run on
+            the [orion|hercules]-login-1 head node.
+
+    -e "your@email.com" Email address to place in the crontab.
+       If this option is not specified, then the existing email address in
+       the crontab will be preserved.
+
+    -v Verbose mode.  Prints output of all commands to stdout.
+
+    -V Very verbose mode.  Passes -v to all commands and prints to stdout.
+
+    -d Debug mode.  Same as -V but also enables logging (set -x).
+
+    -h Display this message.
+EOF
+}
+
+set -eu
+
+# Set default options
+HOMEgfs=""
+_specified_home=false
+_build=false
+_build_flags=""
+_explicit_build_flags=false
+_update_submods=false
+declare -a _yaml_list=("C48_ATM")
+_specified_yaml_list=false
+_yaml_dir=""  # Will be set based off of HOMEgfs if not specified explicitly
+_specified_yaml_dir=false
+_run_all_gfs=false
+_run_all_gefs=false
+_run_all_sfs=false
+_hpc_account=""
+_set_account=false
+_update_cron=false
+_email=""
+_set_email=false
+_verbose=false
+_very_verbose=false
+_verbose_flag="--"
+_debug="false"
+_cwd=$(pwd)
+_runtests="${RUNTESTS:-${_runtests:-}}"
+_nonflag_option_count=0
+
+while [[ $# -gt 0 && "$1" != "--" ]]; do
+   while getopts ":H:bB:uy:Y:GESA:ce:vVdh" option; do
+      case "${option}" in
+        H)
+           HOMEgfs="${OPTARG}"
+           _specified_home=true
+           if [[ ! -d "${HOMEgfs}" ]]; then
+              echo "Specified HOMEgfs directory (${HOMEgfs}) does not exist"
+              exit 1
+           fi
+           ;;
+        b) _build=true ;;
+        B) _build_flags="${OPTARG}" && _explicit_build_flags=true ;;
+        u) _update_submods=true ;;
+        y) # Start over with an empty _yaml_list
+           declare -a _yaml_list=()
+           for _yaml in ${OPTARG}; do
+              # Strip .yaml from the end of each and append to _yaml_list
+              _yaml_list+=("${_yaml//.yaml/}")
+           done
+           _specified_yaml_list=true
+           ;;
+        Y) _yaml_dir="${OPTARG}" && _specified_yaml_dir=true ;;
+        G) _run_all_gfs=true ;;
+        E) _run_all_gefs=true ;;
+        S) _run_all_sfs=true ;;
+        c) _update_cron=true ;;
+        e) _email="${OPTARG}" && _set_email=true ;;
+        v) _verbose=true ;;
+        V) _very_verbose=true && _verbose=true && _verbose_flag="-v" ;;
+        d) _debug=true && _very_verbose=true && _verbose=true && _verbose_flag="-v" && PS4='${LINENO}: ' ;;
+        h) _usage && exit 0 ;;
+        :)
+          echo "[${BASH_SOURCE[0]}]: ${option} requires an argument"
+          _usage
+          ;;
+        *)
+          echo "[${BASH_SOURCE[0]}]: Unrecognized option: ${option}"
+          _usage
+          ;;
+      esac
+   done
+
+   if [[ ${OPTIND:-0} -gt 0 ]]; then
+      shift $((OPTIND-1))
+   fi
+
+   while [[ $# -gt 0 && ! "$1" =~ ^- ]]; do
+      _runtests=${1}
+      (( _nonflag_option_count += 1 ))
+      if [[ ${_nonflag_option_count} -gt 1 ]]; then
+         echo "Too many arguments specified."
+         _usage
+         exit 2
+      fi
+      shift
+   done
+done
+
+function send_email() {
+   # Send an email to $_email.
+   # Only use this once we get to the long steps (building, etc) and on success.
+   _subject="${_subject:-generate_workflows.sh failure on ${machine}}"
+   _body="${1}"
+
+   echo "${_body}" | mail -s "${_subject}" "${_email}"
+}
+
+if [[ -z "${_runtests}" ]]; then
+   echo "Mising run directory (RUNTESTS) argument/environment variable."
+   sleep 2
+   _usage
+   exit 3
+fi
+
+# Turn on logging if running in debug mode
+if [[ "${_debug}" == "true" ]]; then
+   set -x
+fi
+
+# Create the RUNTESTS directory
+[[ "${_verbose}" == "true" ]] && printf "Creating RUNTESTS in %s\n\n" "${_runtests}"
+if [[ ! -d "${_runtests}" ]]; then
+   set +e
+   if ! mkdir -p "${_runtests}" "${_verbose_flag}"; then
+      echo "Unable to create RUNTESTS directory: ${_runtests}"
+      echo "Rerun with -h for usage examples."
+      exit 4
+   fi
+   set -e
+else
+   echo "The RUNTESTS directory ${_runtests} already exists."
+   echo "Would you like to remove it?"
+   _attempts=0
+   while read -r _from_stdin
+   do
+      if [[ "${_from_stdin^^}" =~ Y ]]; then
+         rm -rf "${_runtests}"
+         mkdir -p "${_runtests}"
+         break
+      elif [[ "${_from_stdin^^}" =~ N ]]; then
+         echo "Continuing without removing the directory"
+         break
+      else
+         (( _attempts+=1 ))
+         if [[ ${_attempts} == 3 ]]; then
+            echo "Exiting."
+            exit 99
+         fi
+         echo "'${_from_stdin}' is not a valid choice.  Please type Y or N"
+      fi
+   done
+fi
+
+# Test if multiple "run_all" options were set
+_count_run_alls=0
+[[ "${_run_all_gfs}" == "true" ]] && ((_count_run_alls+=1))
+[[ "${_run_all_gefs}" == "true" ]] && ((_count_run_alls+=1))
+[[ "${_run_all_sfs}" == "true" ]] && ((_count_run_alls+=1))
+
+if (( _count_run_alls > 1 )) ; then
+   echo "Only one run all option (-G -E -S) may be specified"
+   echo "Rerun with just one option and/or with -h for usage examples"
+   exit 5
+fi
+
+# If -S is specified, exit (for now).
+# TODO when SFS tests come online, enable this option.
+if [[ "${_run_all_sfs}" == "true" ]]; then
+   echo "There are no known SFS tests at this time.  Aborting."
+   echo "If you have prepared YAMLs for SFS cases, specify their"
+   echo "location and names without '-S', e.g."
+   echo "generate_workflows.sh -y \"C48_S2S_SFS\" -Y \"/path/to/yaml/directory\""
+   exit 0
+fi
+
+# Set HOMEgfs if it wasn't set by the user
+if [[ "${_specified_home}" == "false" ]]; then
+   script_relpath="$(dirname "${BASH_SOURCE[0]}")"
+   HOMEgfs="$(cd "${script_relpath}/.." && pwd)"
+   [[ "${_verbose}" == "true" ]] && printf "Setting HOMEgfs to %s\n\n" "${HOMEgfs}"
+fi
+
+# Set the _yaml_dir to HOMEgfs/ci/cases/pr if not explicitly set
+[[ "${_specified_yaml_dir}" == false ]] && _yaml_dir="${HOMEgfs}/ci/cases/pr"
+
+function select_all_yamls()
+{
+   # A helper function to select all of the YAMLs for a specified system (gfs, gefs, sfs)
+
+   # This function is called if -G, -E, or -S are specified either with or without a
+   # specified YAML list.  If a YAML list was specified, this function will remove any
+   # YAMLs in that list that are not for the specified system and issue warnings when
+   # doing so.
+
+   _system="${1}"
+   _SYSTEM="${_system^^}"
+
+   # Bash cannot return an array from a function and any edits are descoped at
+   # the end of the function, so use a nameref instead.
+   local -n _nameref_yaml_list='_yaml_list'
+
+   if [[ "${_specified_yaml_list}" == false ]]; then
+      # Start over with an empty _yaml_list
+      _nameref_yaml_list=()
+      printf "Running all %s cases in %s\n\n" "${_SYSTEM}" "${_yaml_dir}"
+      _yaml_count=0
+
+      for _full_path in "${_yaml_dir}/"*.yaml; do
+         # Skip any YAML that isn't supported
+         if ! grep -l "system: *${_system}" "${_full_path}" >& /dev/null ; then continue; fi
+
+         # Select only cases for the specified system
+         _yaml=$(basename "${_full_path}")
+         # Strip .yaml from the filename to get the case name
+         _yaml="${_yaml//.yaml/}"
+         _nameref_yaml_list+=("${_yaml}")
+         [[ "${_verbose}" == true ]] && echo "Found test ${_yaml//.yaml/}"
+         (( _yaml_count+=1 ))
+      done
+
+      if [[ ${_yaml_count} -eq 0 ]]; then
+         read -r -d '' _message << EOM
+            "No YAMLs or ${_SYSTEM} were found in the directory (${_yaml_dir})!"
+            "Please check the directory/YAMLs and try again"
+EOM
+         echo "${_message}"
+         if [[ "${_set_email}" == true ]]; then
+            send_email "${_message}"
+         fi
+         exit 6
+      fi
+   else
+      # Check if the specified yamls are for the specified system
+      for i in "${!_nameref_yaml_list}"; do
+         _yaml="${_nameref_yaml_list[${i}]}"
+         _found=$(grep -l "system: *${system}" "${_yaml_dir}/${_yaml}.yaml")
+         if [[ -z "${_found}" ]]; then
+            echo "WARNING the yaml file ${_yaml_dir}/${_yaml}.yaml is not designed for the ${_SYSTEM} system"
+            echo "Removing this yaml from the set of cases to run"
+            unset '_nameref_yaml_list[${i}]'
+            # Sleep 2 seconds to give the user a moment to react
+            sleep 2s
+         fi
+      done
+   fi
+}
+
+# Check if running all GEFS cases
+if [[ "${_run_all_gefs}" == "true" ]]; then
+   # Append -w to build_all.sh flags if -E was specified
+   if [[ "${_explicit_build_flags}" == "false" && "${_build}" == "true" ]]; then
+       _build_flags="-w"
+   fi
+
+   select_all_yamls "gefs"
+fi
+
+# Check if running all SFS cases
+if [[ "${_run_all_gfs}" == "true" ]]; then
+   # Append -g -u to build_all.sh flags if -G was specified
+   if [[ "${_explicit_build_flags}" == "false" && "${_build}" == "true" ]]; then
+      _build_flags="-g -u"
+   fi
+
+   select_all_yamls "gfs"
+fi
+
+# Loading modules sometimes raises unassigned errors, so disable checks
+set +u
+[[ "${_verbose}" == "true" ]] && printf "Loading modules\n\n"
+[[ "${_debug}" == "true" ]] && set +x
+if ! source "${HOMEgfs}/workflow/gw_setup.sh" >& stdout; then
+   cat stdout
+   echo "Failed to source ${HOMEgfs}/workflow/gw_setup.sh!"
+   exit 7
+fi
+[[ "${_verbose}" == "true" ]] && cat stdout
+rm -f stdout
+[[ "${_debug}" == "true" ]] && set -x
+set -u
+machine=${MACHINE_ID}
+. "${HOMEgfs}/ci/platforms/config.${machine}"
+
+# If _yaml_dir is not set, set it to $HOMEgfs/ci/cases/pr
+if [[ -z ${_yaml_dir} ]]; then
+   _yaml_dir="${HOMEgfs}/ci/cases/pr"
+fi
+
+# Update submodules if requested
+if [[ "${_update_submods}" == "true" ]]; then
+   printf "Updating submodules\n\n"
+   _git_cmd="git submodule update --init --recursive -j 10"
+   if [[ "${_verbose}" == true ]]; then
+      ${_git_cmd}
+   else
+      if ! ${_git_cmd} 2> stderr 1> stdout; then
+         cat stdout stderr
+         read -r -d '' _message << EOM
+The git command (${_git_cmd}) failed with a non-zero status
+Messages from git:
+EOM
+         _newline=$'\n'
+         _message="${_message}${_newline}$(cat stdout stderr)"
+         if [[ "${_set_email}" == true ]]; then
+            send_email "${_message}"
+         fi
+         echo "${_message}"
+         rm -f stdout stderr
+         exit 8
+      fi
+      rm -f stdout stderr
+   fi
+fi
+
+# Build the system if requested
+if [[ "${_build}" == "true" ]]; then
+   printf "Building via build_all.sh %s\n\n" "${_build_flags}"
+   # Let the output of build_all.sh go to stdout regardless of verbose options
+   #shellcheck disable=SC2086,SC2248
+   ${HOMEgfs}/sorc/build_all.sh ${_verbose_flag} ${_build_flags}
+fi
+
+# Link the workflow silently unless there's an error
+[[ "${_verbose}" == true ]] && printf "Linking the workflow\n\n"
+if ! "${HOMEgfs}/sorc/link_workflow.sh" >& stdout; then
+   cat stdout
+   echo "link_workflow.sh failed!"
+   if [[ "${_set_email}" == true ]]; then
+      _stdout=$(cat stdout)
+      send_email "link_workflow.sh failed with the message"$'\n'"${_stdout}"
+   fi
+   rm -f stdout
+   exit 9
+fi
+rm -f stdout
+
+# Configure the environment for running create_experiment.py
+[[ "${_verbose}" == true ]] && printf "Setting up the environment to run create_experiment.py\n\n"
+for i in "${!_yaml_list[@]}"; do
+   _yaml_file="${_yaml_dir}/${_yaml_list[${i}]}.yaml"
+   # Verify that the YAMLs are where we are pointed
+   if [[ ! -s "${_yaml_file}" ]]; then
+      echo "The YAML file ${_yaml_file} does not exist!"
+      echo "Please check the input yaml list and directory."
+      if [[ "${_set_email}" == true ]]; then
+         read -r -d '' _message << EOM
+         generate_workflows.sh failed to find one of the specified YAMLs (${_yaml_file})
+         in the specified YAML directory (${_yaml_dir}).
+EOM
+         send_email "${_message}"
+      fi
+      exit 10
+   fi
+
+   # Strip any unsupported tests
+   _unsupported_systems=$(sed '1,/skip_ci_on_hosts/ d' "${_yaml_file}")
+
+   for _system in ${_unsupported_systems}; do
+      if [[ "${_system}" =~ ${machine} ]]; then
+         if [[ "${_specified_yaml_list}" == true ]]; then
+            printf "WARNING %s is unsupported on %s, removing from case list\n\n" "${_yaml}" "${machine}"
+            if [[ "${_set_email}" == true ]]; then
+               _final_message="${_final_message:-}"$'\n'"The specified YAML case ${_yaml} is not supported on ${machine} and was skipped."
+            fi
+            # Sleep so the user has a moment to notice
+            sleep 2s
+         fi
+         unset '_yaml_list[${i}]'
+         break
+      fi
+   done
+done
+
+# Update the account if specified
+[[ "${_set_account}" == true ]] && export HPC_ACCOUNT=${_hpc_account} && \
+   [[ "${_verbose}" == true ]] && printf "Setting HPC account to %s\n\n" "${HPC_ACCOUNT}"
+
+# Create the experiments
+rm -f "tests.cron" "${_verbose_flag}"
+echo "Running create_experiment.py for ${#_yaml_list[@]} cases"
+
+[[ "${_verbose}" == true ]] && printf "Selected cases: %s\n\n" "${_yaml_list[*]}"
+for _case in "${_yaml_list[@]}"; do
+   [[ "${_verbose}" == false ]] && echo "${_case}"
+   _create_exp_cmd="./create_experiment.py -y ../ci/cases/pr/${_case}.yaml --overwrite"
+   if [[ "${_verbose}" == true ]]; then
+      pslot=${_case} RUNTESTS=${_runtests} ${_create_exp_cmd}
+   else
+      if ! pslot=${_case} RUNTESTS=${_runtests} ${_create_exp_cmd} 2> stderr 1> stdout; then
+         _output=$(cat stdout stderr)
+         _message="The create_experiment command (${_create_exp_cmd}) failed with a non-zero status.  Output:"
+         _message="${_message}"$'\n'"${_output}"
+         if [[ "${_set_email}" == true ]]; then
+            send_email "${_message}"
+         fi
+         echo "${_message}"
+         rm -f stdout stderr
+         exit 11
+      fi
+      rm -f stdout stderr
+   fi
+   grep "${_case}" "${_runtests}/EXPDIR/${_case}/${_case}.crontab" >> tests.cron
+done
+echo
+
+# Update the cron
+if [[ "${_update_cron}" == "true" ]]; then
+   printf "Updating the existing crontab\n\n"
+   echo
+   rm -f existing.cron final.cron "${_verbose_flag}"
+   touch existing.cron final.cron
+
+   # disable -e in case crontab is empty
+   set +e
+   crontab -l > existing.cron
+   set -e
+
+   if [[ "${_debug}" == "true" ]]; then
+      echo "Existing crontab: "
+      echo "#######################"
+      cat existing.cron
+      echo "#######################"
+   fi
+
+   if [[ "${_set_email}" == "true" ]]; then
+      # Replace the existing email in the crontab
+      [[ "${_verbose}" == "true" ]] && printf "Updating crontab email to %s\n\n" "${_email}"
+      sed -i "/^MAILTO/d" existing.cron
+      echo "MAILTO=\"${_email}\"" >> final.cron
+   fi
+
+   cat existing.cron tests.cron >> final.cron
+
+   if [[ "${_verbose}" == "true" ]]; then
+      echo "Setting crontab to:"
+      echo "#######################"
+      cat final.cron
+      echo "#######################"
+   fi
+
+   crontab final.cron
+else
+   _message="Add the following to your crontab or scrontab to start running:"
+   _cron_tests=$(cat tests.cron)
+   _message="${_message}"$'\n'"${_cron_tests}"
+   echo "${_message}"
+   if [[ "${_set_email}" == true ]]; then
+      final_message="${final_message:-}"$'\n'"${_message}"
+   fi
+fi
+
+# Cleanup
+[[ "${_debug}" == "false" ]] && rm -f final.cron existing.cron tests.cron "${_verbose_flag}"
+
+echo "Success!!"
+if [[ "${_set_email}" == true ]]; then
+   final_message=$'Success!\n'"${final_message:-}"
+   _subject="generate_workflow.sh completed successfully" send_email "${final_message}"
+fi
diff --git a/workflow/setup_expt.py b/workflow/setup_expt.py
index e213394e20..494f5ded4d 100755
--- a/workflow/setup_expt.py
+++ b/workflow/setup_expt.py
@@ -7,14 +7,13 @@
 import os
 import glob
 import shutil
-import warnings
 from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter, SUPPRESS
 
 from hosts import Host
 
 from wxflow import parse_j2yaml
 from wxflow import AttrDict
-from wxflow import to_datetime, to_timedelta, datetime_to_YMDH
+from wxflow import to_datetime, datetime_to_YMDH
 
 
 _here = os.path.dirname(__file__)
@@ -303,7 +302,7 @@ def query_and_clean(dirname, force_clean=False):
     if os.path.exists(dirname):
         print(f'\ndirectory already exists in {dirname}')
         if force_clean:
-            overwrite = True
+            overwrite = "YES"
             print(f'removing directory ........ {dirname}\n')
         else:
             overwrite = input('Do you wish to over-write [y/N]: ')