diff --git a/.github/workflows/test_eessi.yml b/.github/workflows/test_eessi.yml
new file mode 100644
index 0000000000..92b1f71cad
--- /dev/null
+++ b/.github/workflows/test_eessi.yml
@@ -0,0 +1,43 @@
+# documentation: https://help.github.com/en/articles/workflow-syntax-for-github-actions
+name: Tests relying on having EESSI pilot repo mounted
+on: [push, pull_request, workflow_dispatch]
+permissions:
+  contents: read # to fetch code (actions/checkout)
+jobs:
+  eessi_pilot_repo:
+    runs-on: ubuntu-20.04
+    strategy:
+      fail-fast: false
+      matrix:
+        EESSI_VERSION:
+        - 2021.12
+        EESSI_SOFTWARE_SUBDIR:
+        - aarch64/generic
+        - aarch64/graviton2
+        - aarch64/graviton3
+        - x86_64/amd/zen2
+        - x86_64/amd/zen3
+        - x86_64/intel/haswell
+        - x86_64/intel/skylake_avx512
+        - x86_64/generic
+    steps:
+        - name: Check out software-layer repository
+          uses: actions/checkout@93ea575cb5d8a053eaa0ac8fa3b40d7e05a33cc8 # v3.1.0
+
+        - name: Mount EESSI CernVM-FS pilot repository
+          uses: cvmfs-contrib/github-action-cvmfs@d4641d0d591c9a5c3be23835ced2fb648b44c04b # v3.1
+          with:
+              cvmfs_config_package: https://github.com/EESSI/filesystem-layer/releases/download/latest/cvmfs-config-eessi_latest_all.deb
+              cvmfs_http_proxy: DIRECT
+              cvmfs_repositories: pilot.eessi-hpc.org
+
+        - name: Test check_missing_installations.sh script
+          run: |
+              source /cvmfs/pilot.eessi-hpc.org/versions/${{matrix.EESSI_VERSION}}/init/bash
+              module load EasyBuild
+              eb --version
+              export EESSI_PREFIX=/cvmfs/pilot.eessi-hpc.org/versions/${{matrix.EESSI_VERSION}}
+              export EESSI_OS_TYPE=linux
+              export EESSI_SOFTWARE_SUBDIR=${{matrix.EESSI_SOFTWARE_SUBDIR}}
+              env | grep ^EESSI | sort
+              ./check_missing_installations.sh
diff --git a/EESSI-pilot-install-software.sh b/EESSI-pilot-install-software.sh
index d03c2bdce7..57c078f511 100755
--- a/EESSI-pilot-install-software.sh
+++ b/EESSI-pilot-install-software.sh
@@ -118,7 +118,7 @@ else
 fi
 
 echo ">> Configuring EasyBuild..."
-source configure_easybuild
+source $TOPDIR/configure_easybuild
 
 echo ">> Setting up \$MODULEPATH..."
 # make sure no modules are loaded
@@ -421,13 +421,7 @@ fi
 
 $TOPDIR/update_lmod_cache.sh ${EPREFIX} ${EASYBUILD_INSTALLPATH}
 
-echo ">> Checking for missing installations..."
-ok_msg="No missing installations, party time!"
-fail_msg="On no, some installations are still missing, how did that happen?!"
-eb_missing_out=$TMPDIR/eb_missing.out
-$EB --easystack eessi-${EESSI_PILOT_VERSION}.yml --experimental --missing --robot $EASYBUILD_PREFIX/ebfiles_repo | tee ${eb_missing_out}
-grep "No missing modules" ${eb_missing_out} > /dev/null
-check_exit_code $? "${ok_msg}" "${fail_msg}"
+$TOPDIR/check_missing_installations.sh
 
 echo ">> Cleaning up ${TMPDIR}..."
 rm -r ${TMPDIR}
diff --git a/check_missing_installations.sh b/check_missing_installations.sh
new file mode 100755
index 0000000000..30f9cc6ff7
--- /dev/null
+++ b/check_missing_installations.sh
@@ -0,0 +1,31 @@
+#!/bin/bash
+#
+# Script to check for missing installations in EESSI pilot software stack (version 2021.12)
+#
+# author: Kenneth Hoste (@boegel)
+#
+# license: GPLv2
+#
+
+TOPDIR=$(dirname $(realpath $0))
+
+if [ -z ${EESSI_PILOT_VERSION} ]; then
+    echo "ERROR: \${EESSI_PILOT_VERSION} must be set to run $0!" >&2
+    exit 1
+fi
+
+LOCAL_TMPDIR=$(mktemp -d)
+
+source $TOPDIR/utils.sh
+
+source $TOPDIR/configure_easybuild
+
+echo ">> Checking for missing installations in ${EASYBUILD_INSTALLPATH}..."
+ok_msg="No missing installations, party time!"
+fail_msg="On no, some installations are still missing, how did that happen?!"
+eb_missing_out=$LOCAL_TMPDIR/eb_missing.out
+# we need to use --from-pr to pull in some easyconfigs that are not available in EasyBuild version being used
+# PR #16531: Nextflow-22.10.1.eb
+${EB:-eb} --from-pr 16531 --easystack eessi-${EESSI_PILOT_VERSION}.yml --experimental --missing | tee ${eb_missing_out}
+grep "No missing modules" ${eb_missing_out} > /dev/null
+check_exit_code $? "${ok_msg}" "${fail_msg}"