From def4c7c01f18dc3a676d9c6ac8632b04e2787b84 Mon Sep 17 00:00:00 2001
From: David Huber <david.huber@noaa.gov>
Date: Tue, 27 Jan 2026 09:57:52 -0500
Subject: [PATCH 01/14] Add the dataroot_com_path function

---
 ush/bash_utils.sh | 42 +++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 41 insertions(+), 1 deletion(-)

diff --git a/ush/bash_utils.sh b/ush/bash_utils.sh
index 48007623351..9bec838a63f 100755
--- a/ush/bash_utils.sh
+++ b/ush/bash_utils.sh
@@ -36,7 +36,9 @@ function declare_from_tmpl() {
     #       MEMDIR='mem001' YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
     #           COMOUT_ATMOS_HISTORY:COM_ATMOS_HISTORY_TMPL
     #
-    if [[ ${DEBUG_WORKFLOW:-"NO"} == "NO" ]]; then set +x; fi
+    if [[ ${DEBUG_WORKFLOW:-"NO"} == "NO" ]]; then
+        set +x
+    fi
     local opts="-g"
     local OPTIND=1
     while getopts "rx" option; do
@@ -110,7 +112,45 @@ function wait_for_file() {
     return 1
 }
 
+# This utility is to be used to create a COM structure in the DATAROOT
+# It will replace the root path (up to $ROTDIR) with $DATAROOT
+# Use realpath --relative-to to get the relative path from $ROTDIR to the target file
+# and then prepend $DATAROOT to that path to get the new target path
+function dataroot_com_path() {
+    #
+    # Generate a COM path in the DATAROOT based on an existing COM path.
+    #
+    # This function takes an existing COM path and generates a corresponding
+    # path in the DATAROOT by replacing the root directory with DATAROOT.
+    #
+    # Syntax:
+    #   dataroot_com_path original_com_path
+    #
+    #   original_com_path: The original COM path to be transformed.
+    #
+    # Example:
+    #   # Declare COMOUT_ATMOS_ANALYSIS using template
+    #   YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
+    #       COMOUT_ATMOS_ANALYSIS:COM_ATMOS_ANALYSIS_TMPL
+    #   # Get the DATAROOT version of the COM path
+    #   pCOMOUT_ATMOS_ANALYSIS=$(dataroot_com_path "${COMOUT_ATMOS_ANALYSIS}")
+    #   echo "New COM path in DATAROOT: ${pCOMOUT_ATMOS_ANALYSIS}"
+    #
+    local original_com_path=${1:?"dataroot_com_path() requires an original COM path"}
+
+    if [[ -z "${ROTDIR:-}" || -z "${DATAROOT:-}" ]]; then
+        echo "FATAL ERROR in dataroot_com_path: ROTDIR and DATAROOT must be defined!"
+        exit 2
+    fi
+
+    local relative_path=$(realpath --relative-to="${ROTDIR}" "${original_com_path}")
+    local new_com_path="${DATAROOT}/${relative_path}"
+
+    echo "${new_com_path}"
+}
+
 # shellcheck disable=
 
 declare -xf declare_from_tmpl
 declare -xf wait_for_file
+declare -xf dataroot_com_path

From 4c2db2734ba9672a2ccb9eb7dad273171dfd40e3 Mon Sep 17 00:00:00 2001
From: David Huber <david.huber@noaa.gov>
Date: Tue, 27 Jan 2026 10:51:56 -0500
Subject: [PATCH 02/14] Declare on separate lines from command

---
 ush/bash_utils.sh | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/ush/bash_utils.sh b/ush/bash_utils.sh
index 9bec838a63f..964a4f59004 100755
--- a/ush/bash_utils.sh
+++ b/ush/bash_utils.sh
@@ -136,14 +136,22 @@ function dataroot_com_path() {
     #   pCOMOUT_ATMOS_ANALYSIS=$(dataroot_com_path "${COMOUT_ATMOS_ANALYSIS}")
     #   echo "New COM path in DATAROOT: ${pCOMOUT_ATMOS_ANALYSIS}"
     #
-    local original_com_path=${1:?"dataroot_com_path() requires an original COM path"}
+
+    if [[ $# -ne 1 ]]; then
+        echo "FATAL ERROR in dataroot_com_path: Incorrect number of arguments!"
+        echo "Usage: dataroot_com_path original_com_path"
+        exit 2
+    fi
+
+    local original_com_path=${1}
 
     if [[ -z "${ROTDIR:-}" || -z "${DATAROOT:-}" ]]; then
         echo "FATAL ERROR in dataroot_com_path: ROTDIR and DATAROOT must be defined!"
         exit 2
     fi
 
-    local relative_path=$(realpath --relative-to="${ROTDIR}" "${original_com_path}")
+    local relative_path
+    relative_path=$(realpath --relative-to="${ROTDIR}" "${original_com_path}")
     local new_com_path="${DATAROOT}/${relative_path}"
 
     echo "${new_com_path}"

From 4074fb731964098ffd39c2e55352af56d8967283 Mon Sep 17 00:00:00 2001
From: David Huber <david.huber@noaa.gov>
Date: Tue, 27 Jan 2026 16:18:12 -0500
Subject: [PATCH 03/14] Use DATAROOT for gsidiags

---
 dev/jobs/JGLOBAL_ATMOS_ANALYSIS        |  7 ++++++
 dev/jobs/JGLOBAL_ATMOS_ANALYSIS_DIAG   |  5 +++++
 dev/scripts/exglobal_atmos_analysis.sh | 31 ++++++++++++++++----------
 dev/scripts/exglobal_diag.sh           | 14 ++++++------
 4 files changed, 38 insertions(+), 19 deletions(-)

diff --git a/dev/jobs/JGLOBAL_ATMOS_ANALYSIS b/dev/jobs/JGLOBAL_ATMOS_ANALYSIS
index 88dc666d4b6..6cb509d6b2a 100755
--- a/dev/jobs/JGLOBAL_ATMOS_ANALYSIS
+++ b/dev/jobs/JGLOBAL_ATMOS_ANALYSIS
@@ -45,6 +45,13 @@ if [[ ! -f "${ATMGES}" ]]; then
     err_exit "FILE MISSING: ATMGES == ${ATMGES}"
 fi
 
+export GENDIAG="${GENDIAG:-YES}"
+
+# Create a DATAROOT directory variable for the gsidiags if GENDIAG is YES
+if [[ "${GENDIAG}" == "YES" ]]; then
+    export pCOMOUT_ATMOS_ANALYSIS="$(dataroot_com_path "${COMOUT_ATMOS_ANALYSIS}")"
+fi
+
 # Get LEVS
 export LEVS
 LEVS=$(${NCLEN} "${ATMGES}" pfull) && true
diff --git a/dev/jobs/JGLOBAL_ATMOS_ANALYSIS_DIAG b/dev/jobs/JGLOBAL_ATMOS_ANALYSIS_DIAG
index 553a58e1160..23e26dd7ce0 100755
--- a/dev/jobs/JGLOBAL_ATMOS_ANALYSIS_DIAG
+++ b/dev/jobs/JGLOBAL_ATMOS_ANALYSIS_DIAG
@@ -26,6 +26,11 @@ YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
     COMOUT_ATMOS_ANALYSIS:COM_ATMOS_ANALYSIS_TMPL
 mkdir -m 775 -p "${COMOUT_ATMOS_ANALYSIS}"
 
+# Create a DATAROOT directory variable where the gsidiags live
+if [[ "${GENDIAG}" == "YES" ]]; then
+    export pCOMIN_ATMOS_ANALYSIS="$(dataroot_com_path "${COMIN_ATMOS_ANALYSIS}")"
+fi
+
 ###############################################################
 # Run relevant script
 ${ANALDIAGSH:-${SCRgfs}/exglobal_diag.sh} && true
diff --git a/dev/scripts/exglobal_atmos_analysis.sh b/dev/scripts/exglobal_atmos_analysis.sh
index 7ce7ede9db7..b556cb3bd6b 100755
--- a/dev/scripts/exglobal_atmos_analysis.sh
+++ b/dev/scripts/exglobal_atmos_analysis.sh
@@ -198,7 +198,6 @@ RUN_SELECT=${RUN_SELECT:-"NO"}
 USE_SELECT=${USE_SELECT:-"NO"}
 USE_RADSTAT=${USE_RADSTAT:-"YES"}
 SELECT_OBS=${SELECT_OBS:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}obsinput.tar}
-GENDIAG=${GENDIAG:-"YES"}
 
 # Set script / GSI control parameters
 DOHYBVAR=${DOHYBVAR:-"NO"}
@@ -882,6 +881,25 @@ if [[ "${SENDDBN}" == "YES" ]]; then
     fi
 fi
 
+if [[ "${GENDIAGS}" == "YES" ]]; then
+    # Move the gsidiags dir.* directories to pCOMOUT_ATMOS_ANALYSIS for diagnostic jobs
+    gsidiags_dir="${pCOMOUT_ATMOS_ANALYSIS}/gsidiags"
+    # First, check that the directories exist
+    count_dirs=$(find . -maxdepth 1 -type d -name 'dir.????' | wc -l)
+    if [[ ${count_dirs:-0} -gt 0 ]]; then
+        mkdir -p "${gsidiags_dir}"
+        for dir in dir.????; do
+            mv "${dir}" "${gsidiags_dir}/"
+            export err=$?
+            if [[ ${err} -ne 0 ]]; then
+                err_exit "Failed to move ${dir} to ${gsidiags_dir}/"
+            fi
+        done
+    else
+        echo "WARNING: No gsidiags dir.* directories found to move."
+    fi
+fi
+
 ################################################################################
 # Postprocessing
 cd "${DATA}" || exit 1
@@ -895,17 +913,6 @@ if [[ "${SENDECF}" == "YES" && "${RUN}" != "enkf" ]]; then
     ecflow_client --event release_fcst
 fi
 
-# Diagnostic files
-# if requested, GSI diagnostic file directories for use later
-if [[ "${GENDIAG}" == "YES" ]]; then
-    tar -cvf gsidiags.tar dir.????
-    export err=$?
-    if [[ ${err} -ne 0 ]]; then
-        err_exit "Failed to tar GSI diagnostic directories!"
-    fi
-    cpfs gsidiags.tar "${COMOUT_ATMOS_ANALYSIS}/${APREFIX}gsidiags${DIAG_SUFFIX:-}.tar"
-fi
-
 echo "${rCDUMP} ${PDY}${cyc} atminc done at $(date)" > "${COMOUT_ATMOS_ANALYSIS}/${APREFIX}increment.done.txt"
 
 ################################################################################
diff --git a/dev/scripts/exglobal_diag.sh b/dev/scripts/exglobal_diag.sh
index 4d9aa5de94e..2a5cc42e273 100755
--- a/dev/scripts/exglobal_diag.sh
+++ b/dev/scripts/exglobal_diag.sh
@@ -39,7 +39,7 @@ rm -f "${RADSTAT}" "${PCPSTAT}" "${CNVSTAT}" "${OZNSTAT}"
 
 # Obs diag
 GENDIAG=${GENDIAG:-"YES"}
-GSIDIAG=${GSIDIAG:-"${COMIN_ATMOS_ANALYSIS}/${APREFIX}gsidiags${DIAG_SUFFIX:-}.tar"}
+GSIDIAGDIR=${GSIDIAGDIR:-"${pCOMIN_ATMOS_ANALYSIS}/gsidiags"}
 USE_BUILD_GSINFO=${USE_BUILD_GSINFO:-"NO"}
 DIAG_COMPRESS=${DIAG_COMPRESS:-"YES"}
 if [[ "${DIAG_COMPRESS:-}" == "YES" ]]; then
@@ -56,13 +56,13 @@ if [[ "${GENDIAG}" != "YES" ]]; then
 fi
 
 ################################################################################
-# Copy gsidiags.tar file from COMIN to DATA and untar
-cpreq "${GSIDIAG}" ./gsidiags.tar
-tar -xvf gsidiags.tar
-export err=$?
-if [[ ${err} -ne 0 ]]; then
-    err_exit "Unable to unpack gsidiags.tar file!"
+# Link to the gsidiags directory if it is populated
+count_dirs=$(find "${GSIDIAGDIR}" -maxdepth 1 -type d -name "dir.*" | wc -l)
+if [[ ${count_dirs} -eq 0 ]]; then
+    export err=1
+    err_exit "No gsidiags directories found in ${GSIDIAGDIR}"
 fi
+${NLN} -sf "${GSIDIAGDIR}" .
 
 # Set up lists and variables for various types of diagnostic files.
 ntype=3

From 9b3dc8941df169b03405eaaaa6609876e39284b3 Mon Sep 17 00:00:00 2001
From: David Huber <david.huber@noaa.gov>
Date: Wed, 28 Jan 2026 14:15:24 -0500
Subject: [PATCH 04/14] Fix tyop in GENDIAG boolean

---
 dev/scripts/exglobal_atmos_analysis.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dev/scripts/exglobal_atmos_analysis.sh b/dev/scripts/exglobal_atmos_analysis.sh
index b556cb3bd6b..7dabfd4facd 100755
--- a/dev/scripts/exglobal_atmos_analysis.sh
+++ b/dev/scripts/exglobal_atmos_analysis.sh
@@ -881,7 +881,7 @@ if [[ "${SENDDBN}" == "YES" ]]; then
     fi
 fi
 
-if [[ "${GENDIAGS}" == "YES" ]]; then
+if [[ "${GENDIAG}" == "YES" ]]; then
     # Move the gsidiags dir.* directories to pCOMOUT_ATMOS_ANALYSIS for diagnostic jobs
     gsidiags_dir="${pCOMOUT_ATMOS_ANALYSIS}/gsidiags"
     # First, check that the directories exist

From 784c76fa828af7918a737fe0bd82aa54cf3bf150 Mon Sep 17 00:00:00 2001
From: David Huber <david.huber@noaa.gov>
Date: Wed, 28 Jan 2026 14:20:13 -0500
Subject: [PATCH 05/14] Use comroot instead of rotdir

---
 ush/bash_utils.sh | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/ush/bash_utils.sh b/ush/bash_utils.sh
index 964a4f59004..d3155e4dfcb 100755
--- a/ush/bash_utils.sh
+++ b/ush/bash_utils.sh
@@ -113,8 +113,8 @@ function wait_for_file() {
 }
 
 # This utility is to be used to create a COM structure in the DATAROOT
-# It will replace the root path (up to $ROTDIR) with $DATAROOT
-# Use realpath --relative-to to get the relative path from $ROTDIR to the target file
+# It will replace the root path (up to $COMROOT) with $DATAROOT
+# Use realpath --relative-to to get the relative path from $COMROOT to the target file
 # and then prepend $DATAROOT to that path to get the new target path
 function dataroot_com_path() {
     #
@@ -145,13 +145,13 @@ function dataroot_com_path() {
 
     local original_com_path=${1}
 
-    if [[ -z "${ROTDIR:-}" || -z "${DATAROOT:-}" ]]; then
-        echo "FATAL ERROR in dataroot_com_path: ROTDIR and DATAROOT must be defined!"
+    if [[ -z "${COMROOT:-}" || -z "${DATAROOT:-}" ]]; then
+        echo "FATAL ERROR in dataroot_com_path: COMROOT and DATAROOT must be defined!"
         exit 2
     fi
 
     local relative_path
-    relative_path=$(realpath --relative-to="${ROTDIR}" "${original_com_path}")
+    relative_path=$(realpath --relative-to="${COMROOT}" "${original_com_path}")
     local new_com_path="${DATAROOT}/${relative_path}"
 
     echo "${new_com_path}"

From 8dcbe683c889267524d4a67b961b070fbe6e3b6f Mon Sep 17 00:00:00 2001
From: David Huber <david.huber@noaa.gov>
Date: Wed, 28 Jan 2026 15:06:23 -0500
Subject: [PATCH 06/14] Fix typos

---
 dev/jobs/JGLOBAL_ATMOS_ANALYSIS_DIAG | 4 +---
 dev/scripts/exglobal_diag.sh         | 2 +-
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/dev/jobs/JGLOBAL_ATMOS_ANALYSIS_DIAG b/dev/jobs/JGLOBAL_ATMOS_ANALYSIS_DIAG
index 23e26dd7ce0..39a8e8b3dff 100755
--- a/dev/jobs/JGLOBAL_ATMOS_ANALYSIS_DIAG
+++ b/dev/jobs/JGLOBAL_ATMOS_ANALYSIS_DIAG
@@ -27,9 +27,7 @@ YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
 mkdir -m 775 -p "${COMOUT_ATMOS_ANALYSIS}"
 
 # Create a DATAROOT directory variable where the gsidiags live
-if [[ "${GENDIAG}" == "YES" ]]; then
-    export pCOMIN_ATMOS_ANALYSIS="$(dataroot_com_path "${COMIN_ATMOS_ANALYSIS}")"
-fi
+export pCOMIN_ATMOS_ANALYSIS="$(dataroot_com_path "${COMIN_ATMOS_ANALYSIS}")"
 
 ###############################################################
 # Run relevant script
diff --git a/dev/scripts/exglobal_diag.sh b/dev/scripts/exglobal_diag.sh
index 2a5cc42e273..99bcfa9537f 100755
--- a/dev/scripts/exglobal_diag.sh
+++ b/dev/scripts/exglobal_diag.sh
@@ -62,7 +62,7 @@ if [[ ${count_dirs} -eq 0 ]]; then
     export err=1
     err_exit "No gsidiags directories found in ${GSIDIAGDIR}"
 fi
-${NLN} -sf "${GSIDIAGDIR}" .
+${NLN} "${GSIDIAGDIR}/"dir.* .
 
 # Set up lists and variables for various types of diagnostic files.
 ntype=3

From 5e9d5d6b62ef9525c6df80d0600316679b4590c2 Mon Sep 17 00:00:00 2001
From: David Huber <david.huber@noaa.gov>
Date: Wed, 28 Jan 2026 16:09:38 -0500
Subject: [PATCH 07/14] Follow symbolic links

---
 dev/scripts/exglobal_diag.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/dev/scripts/exglobal_diag.sh b/dev/scripts/exglobal_diag.sh
index 99bcfa9537f..dbc513228ba 100755
--- a/dev/scripts/exglobal_diag.sh
+++ b/dev/scripts/exglobal_diag.sh
@@ -153,7 +153,8 @@ for loop in ${loops}; do
             if [[ "${dtype}" == *"avhrr"* ]]; then # recast dtype in avhrr form
                 dtype="avhrr${dtype##avhrr[23]}"
             fi
-            count=$(find ./ -path "./dir.*/${dtype}_${loop}*" -type f -printf "." | wc -c)
+            # -L to follow symlinks, as dir.* are symlinks to gsidiags/dir.*
+            count=$(find -L ./dir.* -path "./dir.*/${dtype}_${loop}*" -type f -printf "." | wc -c)
             if [[ ${count} -eq 0 ]]; then
                 continue
             fi

From 3a75c981c326301f14c26e38cd240a1e1155d8ae Mon Sep 17 00:00:00 2001
From: David Huber <david.huber@noaa.gov>
Date: Wed, 28 Jan 2026 16:21:38 -0500
Subject: [PATCH 08/14] Move diagnostic output after releasing the forecast

---
 dev/scripts/exglobal_atmos_analysis.sh | 30 +++++++++++++-------------
 1 file changed, 15 insertions(+), 15 deletions(-)

diff --git a/dev/scripts/exglobal_atmos_analysis.sh b/dev/scripts/exglobal_atmos_analysis.sh
index 7dabfd4facd..9ea71d4d4f5 100755
--- a/dev/scripts/exglobal_atmos_analysis.sh
+++ b/dev/scripts/exglobal_atmos_analysis.sh
@@ -881,6 +881,21 @@ if [[ "${SENDDBN}" == "YES" ]]; then
     fi
 fi
 
+################################################################################
+# Postprocessing
+cd "${DATA}" || exit 1
+
+##############################################################
+# Add this statement to release the forecast job once the
+# atmopsheric analysis and updated surface RESTARTS are
+# available.  Do not release forecast when RUN=enkf
+##############################################################
+if [[ "${SENDECF}" == "YES" && "${RUN}" != "enkf" ]]; then
+    ecflow_client --event release_fcst
+fi
+
+echo "${rCDUMP} ${PDY}${cyc} atminc done at $(date)" > "${COMOUT_ATMOS_ANALYSIS}/${APREFIX}increment.done.txt"
+
 if [[ "${GENDIAG}" == "YES" ]]; then
     # Move the gsidiags dir.* directories to pCOMOUT_ATMOS_ANALYSIS for diagnostic jobs
     gsidiags_dir="${pCOMOUT_ATMOS_ANALYSIS}/gsidiags"
@@ -900,21 +915,6 @@ if [[ "${GENDIAG}" == "YES" ]]; then
     fi
 fi
 
-################################################################################
-# Postprocessing
-cd "${DATA}" || exit 1
-
-##############################################################
-# Add this statement to release the forecast job once the
-# atmopsheric analysis and updated surface RESTARTS are
-# available.  Do not release forecast when RUN=enkf
-##############################################################
-if [[ "${SENDECF}" == "YES" && "${RUN}" != "enkf" ]]; then
-    ecflow_client --event release_fcst
-fi
-
-echo "${rCDUMP} ${PDY}${cyc} atminc done at $(date)" > "${COMOUT_ATMOS_ANALYSIS}/${APREFIX}increment.done.txt"
-
 ################################################################################
 
 exit "${err}"

From 14459e192196d31a682a57c184a2f0620e89dd19 Mon Sep 17 00:00:00 2001
From: David Huber <david.huber@noaa.gov>
Date: Wed, 28 Jan 2026 16:29:17 -0500
Subject: [PATCH 09/14] Address shellcheck issues

---
 dev/jobs/JGLOBAL_ATMOS_ANALYSIS      | 4 +++-
 dev/jobs/JGLOBAL_ATMOS_ANALYSIS_DIAG | 4 +++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/dev/jobs/JGLOBAL_ATMOS_ANALYSIS b/dev/jobs/JGLOBAL_ATMOS_ANALYSIS
index 6cb509d6b2a..a28a0a91216 100755
--- a/dev/jobs/JGLOBAL_ATMOS_ANALYSIS
+++ b/dev/jobs/JGLOBAL_ATMOS_ANALYSIS
@@ -36,6 +36,7 @@ RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
 MEMDIR='ensstat' RUN=${GDUMP_ENS} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
     COMIN_ATMOS_HISTORY_ENS_PREV:COM_ATMOS_HISTORY_TMPL
 
+# shellcheck disable=SC2153
 mkdir -p "${COMOUT_ATMOS_ANALYSIS}"
 
 export ATMGES="${COMIN_ATMOS_HISTORY_PREV}/${GPREFIX}atm.f006.nc"
@@ -49,7 +50,8 @@ export GENDIAG="${GENDIAG:-YES}"
 
 # Create a DATAROOT directory variable for the gsidiags if GENDIAG is YES
 if [[ "${GENDIAG}" == "YES" ]]; then
-    export pCOMOUT_ATMOS_ANALYSIS="$(dataroot_com_path "${COMOUT_ATMOS_ANALYSIS}")"
+    pCOMOUT_ATMOS_ANALYSIS="$(dataroot_com_path "${COMOUT_ATMOS_ANALYSIS}")"
+    export pCOMOUT_ATMOS_ANALYSIS
 fi
 
 # Get LEVS
diff --git a/dev/jobs/JGLOBAL_ATMOS_ANALYSIS_DIAG b/dev/jobs/JGLOBAL_ATMOS_ANALYSIS_DIAG
index 39a8e8b3dff..0f7eabd9033 100755
--- a/dev/jobs/JGLOBAL_ATMOS_ANALYSIS_DIAG
+++ b/dev/jobs/JGLOBAL_ATMOS_ANALYSIS_DIAG
@@ -27,7 +27,9 @@ YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
 mkdir -m 775 -p "${COMOUT_ATMOS_ANALYSIS}"
 
 # Create a DATAROOT directory variable where the gsidiags live
-export pCOMIN_ATMOS_ANALYSIS="$(dataroot_com_path "${COMIN_ATMOS_ANALYSIS}")"
+# shellcheck disable=SC2153
+pCOMIN_ATMOS_ANALYSIS="$(dataroot_com_path "${COMIN_ATMOS_ANALYSIS}")"
+export pCOMIN_ATMOS_ANALYSIS
 
 ###############################################################
 # Run relevant script

From d75e34761d02971d7b08eb7d28d426acdaeff7f8 Mon Sep 17 00:00:00 2001
From: David Huber <david.huber@noaa.gov>
Date: Fri, 30 Jan 2026 14:03:57 -0500
Subject: [PATCH 10/14] Fix eobs and make diag variable names more consistent

---
 dev/jobs/JGLOBAL_ENKF_SELECT_OBS       |  8 ++++++++
 dev/scripts/exglobal_atmos_analysis.sh | 28 ++++++++++++++++++++------
 dev/scripts/exglobal_diag.sh           | 15 ++++++++++++++
 3 files changed, 45 insertions(+), 6 deletions(-)

diff --git a/dev/jobs/JGLOBAL_ENKF_SELECT_OBS b/dev/jobs/JGLOBAL_ENKF_SELECT_OBS
index af264f7d9c6..50ccef6ee7f 100755
--- a/dev/jobs/JGLOBAL_ENKF_SELECT_OBS
+++ b/dev/jobs/JGLOBAL_ENKF_SELECT_OBS
@@ -48,6 +48,14 @@ if [[ ! -f ${ATMGES_ENSMEAN} ]]; then
     err_exit "FILE MISSING: ATMGES_ENSMEAN == ${ATMGES_ENSMEAN}"
 fi
 
+export GENDIAG="${GENDIAG:-YES}"
+
+# Create a DATAROOT directory variable for the gsidiags if GENDIAG is YES
+if [[ "${GENDIAG}" == "YES" ]]; then
+    pCOMOUT_ATMOS_ANALYSIS="$(dataroot_com_path "${COMOUT_ATMOS_ANALYSIS}")"
+    export pCOMOUT_ATMOS_ANALYSIS
+fi
+
 LEVS=$(${NCLEN} "${ATMGES}" pfull) && true
 export err=$?
 set_strict
diff --git a/dev/scripts/exglobal_atmos_analysis.sh b/dev/scripts/exglobal_atmos_analysis.sh
index 9ea71d4d4f5..5652c452996 100755
--- a/dev/scripts/exglobal_atmos_analysis.sh
+++ b/dev/scripts/exglobal_atmos_analysis.sh
@@ -198,6 +198,7 @@ RUN_SELECT=${RUN_SELECT:-"NO"}
 USE_SELECT=${USE_SELECT:-"NO"}
 USE_RADSTAT=${USE_RADSTAT:-"YES"}
 SELECT_OBS=${SELECT_OBS:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}obsinput.tar}
+GENDIAG=${GENDIAG:-"YES"}
 
 # Set script / GSI control parameters
 DOHYBVAR=${DOHYBVAR:-"NO"}
@@ -412,6 +413,16 @@ else
     echo "not using correlated obs error"
 fi
 
+# If GENDIAG is selected, verify that pCOMOUT_ATMOS_ANALYSIS is set
+if [[ "${GENDIAG}" == "YES" ]]; then
+    if [[ -z "${pCOMOUT_ATMOS_ANALYSIS}" ]]; then
+        export err=1
+        err_exit "pCOMOUT_ATMOS_ANALYSIS must be set when GENDIAG=YES"
+    fi
+    # Make the gsidiags directory to house the GSI diagnostic data
+    GSIDIAGDIR=${GSIDIAGDIR:-"${pCOMOUT_ATMOS_ANALYSIS}/gsidiags"}
+fi
+
 ##############################################################
 # CRTM Spectral and Transmittance coefficients
 mkdir -p crtm_coeffs
@@ -898,16 +909,21 @@ echo "${rCDUMP} ${PDY}${cyc} atminc done at $(date)" > "${COMOUT_ATMOS_ANALYSIS}
 
 if [[ "${GENDIAG}" == "YES" ]]; then
     # Move the gsidiags dir.* directories to pCOMOUT_ATMOS_ANALYSIS for diagnostic jobs
-    gsidiags_dir="${pCOMOUT_ATMOS_ANALYSIS}/gsidiags"
-    # First, check that the directories exist
-    count_dirs=$(find . -maxdepth 1 -type d -name 'dir.????' | wc -l)
+    # First, check that the directories exist (we need at least one, so stop after the first match)
+    count_dirs=$(find . -maxdepth 1 -type d -name 'dir.????' -quit -printf "." | wc -c)
     if [[ ${count_dirs:-0} -gt 0 ]]; then
-        mkdir -p "${gsidiags_dir}"
+        mkdir -p "${GSIDIAGDIR}"
+        err=$?
+
+        if [[ ! -d "${GSIDIAGDIR}" || ${err} -ne 0 ]]; then
+            err_exit "Failed to create gsidiags directory at ${GSIDIAGDIR}"
+        fi
+
         for dir in dir.????; do
-            mv "${dir}" "${gsidiags_dir}/"
+            mv "${dir}" "${GSIDIAGDIR}/"
             export err=$?
             if [[ ${err} -ne 0 ]]; then
-                err_exit "Failed to move ${dir} to ${gsidiags_dir}/"
+                err_exit "Failed to move ${dir} to ${GSIDIAGDIR}/"
             fi
         done
     else
diff --git a/dev/scripts/exglobal_diag.sh b/dev/scripts/exglobal_diag.sh
index dbc513228ba..8fcdc8fae03 100755
--- a/dev/scripts/exglobal_diag.sh
+++ b/dev/scripts/exglobal_diag.sh
@@ -55,6 +55,12 @@ if [[ "${GENDIAG}" != "YES" ]]; then
     exit 0
 fi
 
+# Check that the gsidiags directory exists
+if [[ ! -d "${GSIDIAGDIR}" ]]; then
+    export err=1
+    err_exit "gsidiags directory ${GSIDIAGDIR} does not exist"
+fi
+
 ################################################################################
 # Link to the gsidiags directory if it is populated
 count_dirs=$(find "${GSIDIAGDIR}" -maxdepth 1 -type d -name "dir.*" | wc -l)
@@ -62,6 +68,15 @@ if [[ ${count_dirs} -eq 0 ]]; then
     export err=1
     err_exit "No gsidiags directories found in ${GSIDIAGDIR}"
 fi
+
+# Continue if there is at least one file to process
+# Note -quit stops find after the first match
+count_files=$(find "${GSIDIAGDIR}"/dir.* -maxdepth 1 -type f -quit -printf '.' | wc -c)
+if [[ ${count_files} -eq 0 ]]; then
+    echo "WARNING: No diagnostic files found to process!"
+    exit 0
+fi
+
 ${NLN} "${GSIDIAGDIR}/"dir.* .
 
 # Set up lists and variables for various types of diagnostic files.

From 888b0ed74dad7ddbb195cee57fd48cf1179c587b Mon Sep 17 00:00:00 2001
From: David Huber <david.huber@noaa.gov>
Date: Fri, 30 Jan 2026 14:26:54 -0500
Subject: [PATCH 11/14] Ignore sc2153 message for COM variable

---
 dev/jobs/JGLOBAL_ENKF_SELECT_OBS | 1 +
 1 file changed, 1 insertion(+)

diff --git a/dev/jobs/JGLOBAL_ENKF_SELECT_OBS b/dev/jobs/JGLOBAL_ENKF_SELECT_OBS
index 50ccef6ee7f..0436c5bf868 100755
--- a/dev/jobs/JGLOBAL_ENKF_SELECT_OBS
+++ b/dev/jobs/JGLOBAL_ENKF_SELECT_OBS
@@ -40,6 +40,7 @@ MEMDIR='ensstat' RUN=${GDUMP_ENS} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
 RUN="${GDUMP}" YMD=${gPDY} HH=${gcyc} declare_from_tmpl -r \
     COMIN_ATMOS_ANALYSIS_DET_PREV:COM_ATMOS_ANALYSIS_TMPL
 
+# shellcheck disable=SC2153
 mkdir -p "${COMOUT_ATMOS_ANALYSIS}"
 
 export ATMGES_ENSMEAN="${COMIN_ATMOS_HISTORY_PREV}/${GPREFIX}${GSUFFIX}atm.f006.nc"

From 8dbcd6000aa181456b6ea7026bb25ce999e46494 Mon Sep 17 00:00:00 2001
From: David Huber <david.huber@noaa.gov>
Date: Fri, 30 Jan 2026 14:39:30 -0500
Subject: [PATCH 12/14] Ignore shellcheck 2153

---
 dev/jobs/JGLOBAL_ENKF_SELECT_OBS | 1 +
 1 file changed, 1 insertion(+)

diff --git a/dev/jobs/JGLOBAL_ENKF_SELECT_OBS b/dev/jobs/JGLOBAL_ENKF_SELECT_OBS
index 0436c5bf868..48e96539c6e 100755
--- a/dev/jobs/JGLOBAL_ENKF_SELECT_OBS
+++ b/dev/jobs/JGLOBAL_ENKF_SELECT_OBS
@@ -28,6 +28,7 @@ RUN=${RUN/enkf/} YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
     COMIN_OBS:COM_OBS_TMPL
 MEMDIR='ensstat' YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
     COMOUT_ATMOS_ANALYSIS:COM_ATMOS_ANALYSIS_TMPL
+# shellcheck disable=SC2153
 declare -rx COMOUT_ATMOS_ANALYSIS_ENS="${COMOUT_ATMOS_ANALYSIS}"
 
 RUN=${RUN/enkf/} YMD=${PDY} HH=${cyc} declare_from_tmpl -r \

From c1eac3fe58cc914cd2b6f3dc0920a0da79bbec79 Mon Sep 17 00:00:00 2001
From: DavidHuber-NOAA <david.huber@noaa.gov>
Date: Wed, 4 Feb 2026 12:22:35 +0000
Subject: [PATCH 13/14] Add missing pCOMIN declaration

---
 dev/jobs/JGLOBAL_ENKF_DIAG | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/dev/jobs/JGLOBAL_ENKF_DIAG b/dev/jobs/JGLOBAL_ENKF_DIAG
index fa494dfb847..5e92c7ac56c 100755
--- a/dev/jobs/JGLOBAL_ENKF_DIAG
+++ b/dev/jobs/JGLOBAL_ENKF_DIAG
@@ -29,6 +29,11 @@ MEMDIR="ensstat" YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
     COMIN_ATMOS_ANALYSIS:COM_ATMOS_ANALYSIS_TMPL \
     COMOUT_ATMOS_ANALYSIS:COM_ATMOS_ANALYSIS_TMPL
 
+# Create a DATAROOT directory variable where the gsidiags live
+# shellcheck disable=SC2153
+pCOMIN_ATMOS_ANALYSIS="$(dataroot_com_path "${COMIN_ATMOS_ANALYSIS}")"
+export pCOMIN_ATMOS_ANALYSIS
+
 #RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
 #    COMIN_OBS_PREV:COM_OBS_TMPL \
 #    COMIN_ATMOS_ANALYSIS_DET_PREV:COM_ATMOS_ANALYSIS_TMPL

From aa6873704642a699b5c9b4481a69a1f24aef75cd Mon Sep 17 00:00:00 2001
From: DavidHuber-NOAA <david.huber@noaa.gov>
Date: Wed, 4 Feb 2026 12:23:01 +0000
Subject: [PATCH 14/14] Fix find order

---
 dev/scripts/exglobal_atmos_analysis.sh | 2 +-
 dev/scripts/exglobal_diag.sh           | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/dev/scripts/exglobal_atmos_analysis.sh b/dev/scripts/exglobal_atmos_analysis.sh
index 5652c452996..59879131f81 100755
--- a/dev/scripts/exglobal_atmos_analysis.sh
+++ b/dev/scripts/exglobal_atmos_analysis.sh
@@ -910,7 +910,7 @@ echo "${rCDUMP} ${PDY}${cyc} atminc done at $(date)" > "${COMOUT_ATMOS_ANALYSIS}
 if [[ "${GENDIAG}" == "YES" ]]; then
     # Move the gsidiags dir.* directories to pCOMOUT_ATMOS_ANALYSIS for diagnostic jobs
     # First, check that the directories exist (we need at least one, so stop after the first match)
-    count_dirs=$(find . -maxdepth 1 -type d -name 'dir.????' -quit -printf "." | wc -c)
+    count_dirs=$(find . -maxdepth 1 -type d -name 'dir.????' -printf "." -quit | wc -c)
     if [[ ${count_dirs:-0} -gt 0 ]]; then
         mkdir -p "${GSIDIAGDIR}"
         err=$?
diff --git a/dev/scripts/exglobal_diag.sh b/dev/scripts/exglobal_diag.sh
index 8fcdc8fae03..006515dc554 100755
--- a/dev/scripts/exglobal_diag.sh
+++ b/dev/scripts/exglobal_diag.sh
@@ -71,7 +71,7 @@ fi
 
 # Continue if there is at least one file to process
 # Note -quit stops find after the first match
-count_files=$(find "${GSIDIAGDIR}"/dir.* -maxdepth 1 -type f -quit -printf '.' | wc -c)
+count_files=$(find "${GSIDIAGDIR}"/dir.* -maxdepth 1 -type f -printf '.' -quit | wc -c)
 if [[ ${count_files} -eq 0 ]]; then
     echo "WARNING: No diagnostic files found to process!"
     exit 0