diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index f25c74e9640d78f3e2c5f0a81e7f8b0743cff6b8..7a19fd1a1d89ac8766531626f6f416ffc021aab1 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -5,6 +5,7 @@ variables:
   DETECTOR_CONFIG: epic_craterlake
   GITHUB_SHA: ''
   GITHUB_REPOSITORY: ''
+  SNAKEMAKE_FLAGS: '--cache --rerun-triggers code input params software-env'
 
 workflow:
   name: '$PIPELINE_NAME'
diff --git a/benchmarks/backgrounds/config.yml b/benchmarks/backgrounds/config.yml
index c4d084d795ea6ec31f633cbe6ca225ce09a5c368..79b864bb0515e7e0cb5d2a545335078df23cedac 100644
--- a/benchmarks/backgrounds/config.yml
+++ b/benchmarks/backgrounds/config.yml
@@ -5,7 +5,7 @@ sim:backgrounds:
     - mkdir -p $LOCAL_DATA_PATH/input
     - ln -s $LOCAL_DATA_PATH/input input
     - |
-      snakemake --cache --cores 2 \
+      snakemake $SNAKEMAKE_FLAGS --cores 2 \
         sim_output/$DETECTOR_CONFIG/backgrounds/EPIC/EVGEN/BACKGROUNDS/BEAMGAS/electron/GETaLM1.0.0-1.0/10GeV/GETaLM1.0.0-1.0_ElectronBeamGas_10GeV_foam_emin10keV_run001.edm4hep.root \
         sim_output/$DETECTOR_CONFIG/backgrounds/EPIC/EVGEN/DIS/NC/10x100/minQ2=1/pythia8NCDIS_10x100_minQ2=1_beamEffects_xAngle=-0.025_hiDiv_1.edm4hep.root \
         sim_output/$DETECTOR_CONFIG/backgrounds/EPIC/EVGEN/BACKGROUNDS/BEAMGAS/proton/pythia8.306-1.0/100GeV/pythia8.306-1.0_ProtonBeamGas_100GeV_run001.edm4hep.root
@@ -19,7 +19,7 @@ bench:backgrounds_emcal_backwards:
     - ln -s $LOCAL_DATA_PATH/input input
     - export PYTHONUSERBASE=$LOCAL_DATA_PATH/deps
     - pip install -r benchmarks/backgrounds/requirements.txt
-    - snakemake --cores 8 backgrounds_ecal_backwards
+    - snakemake $SNAKEMAKE_FLAGS --cores 8 backgrounds_ecal_backwards
 
 collect_results:backgrounds:
   extends: .det_benchmark
@@ -29,5 +29,5 @@ collect_results:backgrounds:
   script:
     - ls -lrht
     - mv results{,_save}/ # move results directory out of the way to preserve it
-    - snakemake --cores 1 --delete-all-output backgrounds_ecal_backwards
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 --delete-all-output backgrounds_ecal_backwards
     - mv results{_save,}/
diff --git a/benchmarks/backwards_ecal/config.yml b/benchmarks/backwards_ecal/config.yml
index 9eff9b58355de46c32d3ddb5cfb9af5bc4e09698..7048f8e79d60e37261e56819c87cd99473b3b7fc 100644
--- a/benchmarks/backwards_ecal/config.yml
+++ b/benchmarks/backwards_ecal/config.yml
@@ -16,7 +16,7 @@ sim:backwards_ecal:
         ]
   script:
     - |
-      snakemake --cache --cores 5 sim_output/backwards_ecal/${DETECTOR_CONFIG}/${PARTICLE}/${MOMENTUM}/130to177deg/flag
+      snakemake $SNAKEMAKE_FLAGS --cores 5 sim_output/backwards_ecal/${DETECTOR_CONFIG}/${PARTICLE}/${MOMENTUM}/130to177deg/flag
 
 bench:backwards_ecal:
   extends: .det_benchmark
@@ -26,7 +26,7 @@ bench:backwards_ecal:
   script:
     - export PYTHONUSERBASE=$LOCAL_DATA_PATH/deps
     - pip install -r benchmarks/backwards_ecal/requirements.txt
-    - snakemake --cores 1 backwards_ecal
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 backwards_ecal
 
 collect_results:backwards_ecal:
   extends: .det_benchmark
@@ -36,5 +36,5 @@ collect_results:backwards_ecal:
   script:
     - ls -lrht
     - mv results{,_save}/ # move results directory out of the way to preserve it
-    - snakemake --cores 1 --delete-all-output backwards_ecal
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 --delete-all-output backwards_ecal
     - mv results{_save,}/
diff --git a/benchmarks/barrel_ecal/config.yml b/benchmarks/barrel_ecal/config.yml
index a236f68bb08e7f5063f6ad3691bc5cb3c84213cf..45fc3e1c5281034397ac8834de988dcfe264bafc 100644
--- a/benchmarks/barrel_ecal/config.yml
+++ b/benchmarks/barrel_ecal/config.yml
@@ -2,13 +2,13 @@ sim:emcal_barrel_pions:
   extends: .det_benchmark
   stage: simulate
   script:
-    - snakemake --cores 1 $DETECTOR_CONFIG/sim_output/sim_emcal_barrel_{piplus,piminus}_energies5.0_5.0.edm4hep.root
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 $DETECTOR_CONFIG/sim_output/sim_emcal_barrel_{piplus,piminus}_energies5.0_5.0.edm4hep.root
 
 sim:emcal_barrel_pi0:
   extends: .det_benchmark
   stage: simulate
   script:
-    - snakemake --cores 1 $DETECTOR_CONFIG/sim_output/sim_emcal_barrel_pi0_energies5.0_5.0.edm4hep.root
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 $DETECTOR_CONFIG/sim_output/sim_emcal_barrel_pi0_energies5.0_5.0.edm4hep.root
 
 sim:emcal_barrel_electrons:
   extends: .det_benchmark
@@ -16,20 +16,20 @@ sim:emcal_barrel_electrons:
   script:
     - if [[ "$RUN_EXTENDED_BENCHMARK" == "true" ]] ; then snakemake --cores $DETECTOR_CONFIG/results/energy_scan/emcal_barrel_electron_fsam_scan.png; fi
     - export JUGGLER_N_EVENTS=400
-    - snakemake --cores 1 $DETECTOR_CONFIG/sim_output/sim_emcal_barrel_electron_energies5.0_5.0.edm4hep.root
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 $DETECTOR_CONFIG/sim_output/sim_emcal_barrel_electron_energies5.0_5.0.edm4hep.root
 
 sim:emcal_barrel_photons:
   extends: .det_benchmark
   stage: simulate
   script:
     - if [[ "$RUN_EXTENDED_BENCHMARK" == "true" ]] ; then snakemake --cores $DETECTOR_CONFIG/results/energy_scan/emcal_barrel_proton_fsam_scan.png; fi
-    - snakemake --cores 1 $DETECTOR_CONFIG/sim_output/sim_emcal_barrel_photon_energies5.0_5.0.edm4hep.root
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 $DETECTOR_CONFIG/sim_output/sim_emcal_barrel_photon_energies5.0_5.0.edm4hep.root
 
 sim:emcal_barrel_pion_rejection:
   extends: .det_benchmark
   stage: simulate
   script:
-    - snakemake --cores 1 $DETECTOR_CONFIG/sim_output/sim_emcal_barrel_{piminus,electron}_energies1.0_18.0.edm4hep.root
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 $DETECTOR_CONFIG/sim_output/sim_emcal_barrel_{piminus,electron}_energies1.0_18.0.edm4hep.root
 
 calib:emcal_barrel_electrons:
   extends: .det_benchmark
@@ -39,7 +39,7 @@ calib:emcal_barrel_electrons:
   script:
     - ls -lhtR sim_output/
     - rootls -t sim_output/sim_emcal_barrel_electron_energies5.0_5.0.edm4hep.root
-    - snakemake --cores 1 $DETECTOR_CONFIG/results/emcal_barrel_electron_calibration.json
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 $DETECTOR_CONFIG/results/emcal_barrel_electron_calibration.json
     - mv sim_output/sim_emcal_barrel_electron.edm4hep.root results/.
     - echo "JSON file(s) from analysis:" ; cat results/*.json
 
@@ -49,7 +49,7 @@ bench:emcal_barrel_pions:
   needs:
     - ["sim:emcal_barrel_pions"]
   script:
-    - snakemake --cores 1 $DETECTOR_CONFIG/results/emcal_barrel_pions_Ethr.png
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 $DETECTOR_CONFIG/results/emcal_barrel_pions_Ethr.png
 
 bench:emcal_barrel_electrons_scan:
   extends: .det_benchmark
@@ -66,7 +66,7 @@ bench:emcal_barrel_pi0:
     - ["sim:emcal_barrel_pi0", "calib:emcal_barrel_electrons"]
   script:
     - echo "JSON file(s) from analysis:" ; cat results/*.json
-    - snakemake --cores 1 epic_craterlake/results/Barrel_emcal_pi0.json
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 epic_craterlake/results/Barrel_emcal_pi0.json
 
 bench:emcal_barrel_photons:
   extends: .det_benchmark
@@ -76,7 +76,7 @@ bench:emcal_barrel_photons:
   script:
     - ls -lhtR sim_output/
     - rootls -t sim_output/sim_emcal_barrel_photon_energies5.0_5.0.edm4hep.root
-    - snakemake --cores 1 $DETECTOR_CONFIG/results/emcal_barrel_photon_calibration.json
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 $DETECTOR_CONFIG/results/emcal_barrel_photon_calibration.json
     - mv sim_output/sim_emcal_barrel_photon.edm4hep.root results/.
     - if [[ "$RUN_EXTENDED_BENCHMARK" == "true" ]] ; then snakemake --cores $DETECTOR_CONFIG/results/energy_scan/emcal_barrel_proton_fsam_scan.png; fi
 
@@ -89,7 +89,7 @@ bench:emcal_barrel_pion_rejection:
     - ls -lhtR sim_output/
     - rootls -t $DETECTOR_CONFIG/sim_output/sim_emcal_barrel_piminus_energies1.0_18.0.edm4hep.root
     - rootls -t $DETECTOR_CONFIG/sim_output/sim_emcal_barrel_electron_energies1.0_18.0.edm4hep.root
-    - snakemake --cores 1 $DETECTOR_CONFIG/results/Barrel_emcal_pion_rej.json
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 $DETECTOR_CONFIG/results/Barrel_emcal_pion_rej.json
 
 collect_results:barrel_ecal:
   extends: .det_benchmark
diff --git a/benchmarks/ecal_gaps/config.yml b/benchmarks/ecal_gaps/config.yml
index 9d967c877961c7261a172185d433f2d54e8abdb3..9c0a8a09d6e2d5faaedadac432f7304849ba6508 100644
--- a/benchmarks/ecal_gaps/config.yml
+++ b/benchmarks/ecal_gaps/config.yml
@@ -4,7 +4,7 @@ sim:ecal_gaps:
   script:
     - mkdir -p $LOCAL_DATA_PATH/input
     - ln -s $LOCAL_DATA_PATH/input input
-    - snakemake --cache --cores 10 ecal_gaps --omit-from ecal_gaps
+    - snakemake $SNAKEMAKE_FLAGS --cache --cores 10 ecal_gaps --omit-from ecal_gaps
 
 bench:ecal_gaps:
   extends: .det_benchmark
@@ -15,7 +15,7 @@ bench:ecal_gaps:
     - ln -s $LOCAL_DATA_PATH/input input
     - export PYTHONUSERBASE=$LOCAL_DATA_PATH/deps
     - pip install -r benchmarks/ecal_gaps/requirements.txt
-    - snakemake --cores 8 ecal_gaps
+    - snakemake $SNAKEMAKE_FLAGS --cores 8 ecal_gaps
 
 collect_results:ecal_gaps:
   extends: .det_benchmark
@@ -25,5 +25,5 @@ collect_results:ecal_gaps:
   script:
     - ls -lrht
     - mv results{,_save}/ # move results directory out of the way to preserve it
-    - snakemake --cores 1 --delete-all-output ecal_gaps
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 --delete-all-output ecal_gaps
     - mv results{_save,}/
diff --git a/benchmarks/femc_electron/config.yml b/benchmarks/femc_electron/config.yml
index 7b6f1043faf7e817b560820c1347e1e671892e8e..11c8deea1ba22b2a1f79f657b322a529667df9ac 100644
--- a/benchmarks/femc_electron/config.yml
+++ b/benchmarks/femc_electron/config.yml
@@ -13,7 +13,7 @@ sim:femc_electron:
       - P: 80
   timeout: 1 hours
   script:
-    - snakemake --cores 1 sim_output/femc_electron/epic_craterlake_rec_e-_${P}GeV.edm4eic.root
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 sim_output/femc_electron/epic_craterlake_rec_e-_${P}GeV.edm4eic.root
   retry:
     max: 2
     when:
@@ -24,7 +24,7 @@ bench:femc_electron:
   stage: benchmarks
   needs: ["sim:femc_electron"]
   script:
-    - snakemake --cores 1 results/epic_craterlake/femc_electron
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 results/epic_craterlake/femc_electron
 
 collect_results:femc_electron:
   extends: .det_benchmark
@@ -33,5 +33,5 @@ collect_results:femc_electron:
   script:
     - ls -al
     - mv results{,_save}/ # move results directory out of the way to preserve it
-    - snakemake --cores 1 --delete-all-output results/epic_craterlake/femc_electron
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 --delete-all-output results/epic_craterlake/femc_electron
     - mv results{_save,}/
diff --git a/benchmarks/femc_photon/config.yml b/benchmarks/femc_photon/config.yml
index af710897b9a022555e857227a44dec2c05926489..dca2694ed4a4a5eb92ec821bec34309a2152b827 100644
--- a/benchmarks/femc_photon/config.yml
+++ b/benchmarks/femc_photon/config.yml
@@ -13,7 +13,7 @@ sim:femc_photon:
       - P: 80
   timeout: 1 hours
   script:
-    - snakemake --cores 1 sim_output/femc_photon/epic_craterlake_rec_photon_${P}GeV.edm4eic.root
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 sim_output/femc_photon/epic_craterlake_rec_photon_${P}GeV.edm4eic.root
   retry:
     max: 2
     when:
@@ -24,7 +24,7 @@ bench:femc_photon:
   stage: benchmarks
   needs: ["sim:femc_photon"]
   script:
-    - snakemake --cores 1 results/epic_craterlake/femc_photon
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 results/epic_craterlake/femc_photon
 
 collect_results:femc_photon:
   extends: .det_benchmark
@@ -33,5 +33,5 @@ collect_results:femc_photon:
   script:
     - ls -al
     - mv results{,_save}/ # move results directory out of the way to preserve it
-    - snakemake --cores 1 --delete-all-output results/epic_craterlake/femc_photon
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 --delete-all-output results/epic_craterlake/femc_photon
     - mv results{_save,}/
diff --git a/benchmarks/femc_pi0/config.yml b/benchmarks/femc_pi0/config.yml
index 46e6ed9e73cd3a2606db2445b266cf8c4765f1c9..787cb583dac0d361295146d53891f0c1bd440bbb 100644
--- a/benchmarks/femc_pi0/config.yml
+++ b/benchmarks/femc_pi0/config.yml
@@ -12,7 +12,7 @@ sim:femc_pi0:
       - P: 70
       - P: 80
   script:
-    - snakemake --cores 1 sim_output/femc_pi0/epic_craterlake_rec_pi0_${P}GeV.edm4eic.root
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 sim_output/femc_pi0/epic_craterlake_rec_pi0_${P}GeV.edm4eic.root
   retry:
     max: 2
     when:
@@ -23,7 +23,7 @@ bench:femc_pi0:
   stage: benchmarks
   needs: ["sim:femc_pi0"]
   script:
-    - snakemake --cores 1 results/epic_craterlake/femc_pi0
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 results/epic_craterlake/femc_pi0
 
 collect_results:femc_pi0:
   extends: .det_benchmark
@@ -32,5 +32,5 @@ collect_results:femc_pi0:
   script:
     - ls -al
     - mv results{,_save}/ # move results directory out of the way to preserve it
-    - snakemake --cores 1 --delete-all-output results/epic_craterlake/femc_pi0
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 --delete-all-output results/epic_craterlake/femc_pi0
     - mv results{_save,}/
diff --git a/benchmarks/insert_muon/config.yml b/benchmarks/insert_muon/config.yml
index 76899c1d9e07b193fe41c44f46a0d841f51f85a6..4e3272af2213d0a907620e38256f69a1abcca0fb 100644
--- a/benchmarks/insert_muon/config.yml
+++ b/benchmarks/insert_muon/config.yml
@@ -5,7 +5,7 @@ sim:insert_muon:
     matrix:
       - P: 50
   script:
-    - snakemake --cores 5 sim_output/insert_muon/epic_craterlake_sim_mu-_${P}GeV_{0,1,2,3,4}.edm4hep.root
+    - snakemake $SNAKEMAKE_FLAGS --cores 5 sim_output/insert_muon/epic_craterlake_sim_mu-_${P}GeV_{0,1,2,3,4}.edm4hep.root
   retry:
     max: 2
     when:
@@ -16,7 +16,7 @@ bench:insert_muon:
   stage: benchmarks
   needs: ["sim:insert_muon"]
   script:
-    - snakemake --cores 1 results/epic_craterlake/insert_muon
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 results/epic_craterlake/insert_muon
 
 collect_results:insert_muon:
   extends: .det_benchmark
@@ -25,5 +25,5 @@ collect_results:insert_muon:
   script:
     - ls -al
     - mv results{,_save}/ # move results directory out of the way to preserve it
-    - snakemake --cores 1 --delete-all-output results/epic_craterlake/insert_muon
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 --delete-all-output results/epic_craterlake/insert_muon
     - mv results{_save,}/
diff --git a/benchmarks/insert_neutron/config.yml b/benchmarks/insert_neutron/config.yml
index eedac937686f729f3785bf63dae812fcd2768ce4..90435261a83d4cfa6e9bd4448be2f68f72a933ad 100644
--- a/benchmarks/insert_neutron/config.yml
+++ b/benchmarks/insert_neutron/config.yml
@@ -11,7 +11,7 @@ sim:insert_neutron:
       - P: 70
       - P: 80
   script:
-    - snakemake --cores 5 sim_output/insert_neutron/epic_craterlake_rec_neutron_${P}GeV_{0,1,2,3,4}.edm4eic.root
+    - snakemake $SNAKEMAKE_FLAGS --cores 5 sim_output/insert_neutron/epic_craterlake_rec_neutron_${P}GeV_{0,1,2,3,4}.edm4eic.root
   retry:
     max: 2
     when:
@@ -22,7 +22,7 @@ bench:insert_neutron:
   stage: benchmarks
   needs: ["sim:insert_neutron"]
   script:
-    - snakemake --cores 1 results/epic_craterlake/insert_neutron
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 results/epic_craterlake/insert_neutron
 
 collect_results:insert_neutron:
   extends: .det_benchmark
@@ -31,5 +31,5 @@ collect_results:insert_neutron:
   script:
     - ls -al
     - mv results{,_save}/ # move results directory out of the way to preserve it
-    - snakemake --cores 1 --delete-all-output results/epic_craterlake/insert_neutron
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 --delete-all-output results/epic_craterlake/insert_neutron
     - mv results{_save,}/
diff --git a/benchmarks/lfhcal/config.yml b/benchmarks/lfhcal/config.yml
index a6dfcbe4e52e2348799a9e21dc567605226266ea..8dfc713069b1172ee781f6d978f12a370b8ba571 100644
--- a/benchmarks/lfhcal/config.yml
+++ b/benchmarks/lfhcal/config.yml
@@ -16,7 +16,7 @@ bench:lfhcal:
   needs:
     - ["sim:lfhcal"]
   script:
-    - snakemake --cores 3 lfhcal_local
+    - snakemake $SNAKEMAKE_FLAGS --cores 3 lfhcal_local
 
 collect_results:lfhcal:
   extends: .det_benchmark
@@ -26,7 +26,7 @@ collect_results:lfhcal:
   script:
     - ls -lrht
     - mv results{,_save}/ # move results directory out of the way to preserve it
-    - snakemake --cores 1 --delete-all-output lfhcal_local
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 --delete-all-output lfhcal_local
     - mv results{_save,}/
 
 bench:lfhcal_campaigns:
@@ -34,7 +34,7 @@ bench:lfhcal_campaigns:
   stage: benchmarks
   #when: manual
   script:
-    - snakemake --cores 1 lfhcal_campaigns
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 lfhcal_campaigns
 
 collect_results:lfhcal_campaigns:
   extends: .det_benchmark
@@ -44,5 +44,5 @@ collect_results:lfhcal_campaigns:
   script:
     - ls -lrht
     - mv results{,_save}/ # move results directory out of the way to preserve it
-    - snakemake --cores 1 --delete-all-output lfhcal_campaigns
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 --delete-all-output lfhcal_campaigns
     - mv results{_save,}/
diff --git a/benchmarks/material_scan/config.yml b/benchmarks/material_scan/config.yml
index f8bc0822e5d6dc8047d13bf9cc0071d016b527c7..3c87305e4eda27b73dca417499feab538e76cc86 100644
--- a/benchmarks/material_scan/config.yml
+++ b/benchmarks/material_scan/config.yml
@@ -2,7 +2,7 @@ bench:material_scan:
   extends: .det_benchmark
   stage: benchmarks
   script:
-    - snakemake --cores 1 epic_craterlake/results/material_scan_details.pdf
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 epic_craterlake/results/material_scan_details.pdf
 
 collect_results:material_scan:
   extends: .det_benchmark
diff --git a/benchmarks/tracking_performances/config.yml b/benchmarks/tracking_performances/config.yml
index 90a0d0f6deb2f9b235edfa2b6786b0e641bef298..2419000bd0ec651eae5635b5dc9919b3403a2a2b 100644
--- a/benchmarks/tracking_performances/config.yml
+++ b/benchmarks/tracking_performances/config.yml
@@ -18,7 +18,7 @@ bench:tracking_performance:
   needs:
     - ["sim:tracking_performance"]
   script:
-    - snakemake --cores 3 tracking_performance_local
+    - snakemake $SNAKEMAKE_FLAGS --cores 3 tracking_performance_local
 
 collect_results:tracking_performance:
   extends: .det_benchmark
@@ -27,14 +27,14 @@ collect_results:tracking_performance:
     - "bench:tracking_performance"
   script:
     - ls -lrht
-    - snakemake --cores 1 --delete-all-output tracking_performance_local
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 --delete-all-output tracking_performance_local
 
 bench:tracking_performance_campaigns:
   extends: .det_benchmark
   stage: benchmarks
   #when: manual
   script:
-    - snakemake --cores 1 tracking_performance_campaigns
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 tracking_performance_campaigns
 
 collect_results:tracking_performance_campaigns:
   extends: .det_benchmark
@@ -44,5 +44,5 @@ collect_results:tracking_performance_campaigns:
   script:
     - ls -lrht
     - mv results{,_save}/ # move results directory out of the way to preserve it
-    - snakemake --cores 1 --delete-all-output tracking_performance_campaigns
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 --delete-all-output tracking_performance_campaigns
     - mv results{_save,}/
diff --git a/benchmarks/tracking_performances_dis/config.yml b/benchmarks/tracking_performances_dis/config.yml
index 961df5492dfe5871cea6bd441f6d5b9d23c101f8..066e8df754e8258ead9626d339c720eeafa9bc33 100644
--- a/benchmarks/tracking_performances_dis/config.yml
+++ b/benchmarks/tracking_performances_dis/config.yml
@@ -2,7 +2,7 @@ sim:tracking_performances_dis:
   extends: .det_benchmark
   stage: simulate
   script:
-    - snakemake --cache --cores 5 results/tracking_performances_dis/epic_craterlake_tracking_only/pythia8NCDIS_18x275_minQ2=1_combined_5/hists.root 
+    - snakemake $SNAKEMAKE_FLAGS --cores 5 results/tracking_performances_dis/epic_craterlake_tracking_only/pythia8NCDIS_18x275_minQ2=1_combined_5/hists.root
   retry:
     max: 2
     when:
@@ -14,7 +14,7 @@ bench:tracking_performances_dis:
   needs:
     - ["sim:tracking_performances_dis"]
   script:
-    - snakemake --cores 1 trk_dis_run_locally_trk_only
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 trk_dis_run_locally_trk_only
     # avoid uploading intermediate results
     - find results/tracking_performances_dis/ -mindepth 2 -maxdepth 2 -type d ! -name "*combined*" | xargs rm -rfv
 
@@ -26,7 +26,7 @@ collect_results:tracking_performances_dis:
   script:
     - ls -lrht
     - mv results{,_save}/ # move results directory out of the way to preserve it
-    - snakemake --cores 1 --delete-all-output trk_dis_run_locally_trk_only
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 --delete-all-output trk_dis_run_locally_trk_only
     - mv results{_save,}/
     # convert to png
     - |
diff --git a/benchmarks/zdc_lambda/config.yml b/benchmarks/zdc_lambda/config.yml
index e6b1603166308c01011962fd5b1eafd9f01f9355..609942f5a8ba3b541e906e8afe2865b5387cd00b 100644
--- a/benchmarks/zdc_lambda/config.yml
+++ b/benchmarks/zdc_lambda/config.yml
@@ -12,7 +12,7 @@ sim:zdc_lambda:
       - P: 250
       - P: 275
   script:
-    - snakemake --cores 5 sim_output/zdc_lambda/epic_zdc_sipm_on_tile_only_rec_lambda_dec_${P}GeV_{0,1,2,3,4}.edm4eic.root
+    - snakemake $SNAKEMAKE_FLAGS --cores 5 sim_output/zdc_lambda/epic_zdc_sipm_on_tile_only_rec_lambda_dec_${P}GeV_{0,1,2,3,4}.edm4eic.root
   retry:
     max: 2
     when:
@@ -23,7 +23,7 @@ bench:zdc_lambda:
   stage: benchmarks
   needs: ["sim:zdc_lambda"]
   script:
-    - snakemake --cores 1 results/epic_zdc_sipm_on_tile_only/zdc_lambda
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 results/epic_zdc_sipm_on_tile_only/zdc_lambda
 
 collect_results:zdc_lambda:
   extends: .det_benchmark
@@ -32,5 +32,5 @@ collect_results:zdc_lambda:
   script:
     - ls -al
     - mv results{,_save}/ # move results directory out of the way to preserve it
-    - snakemake --cores 1 --delete-all-output results/epic_zdc_sipm_on_tile_only/zdc_lambda
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 --delete-all-output results/epic_zdc_sipm_on_tile_only/zdc_lambda
     - mv results{_save,}/
diff --git a/benchmarks/zdc_lyso/config.yml b/benchmarks/zdc_lyso/config.yml
index eb0a763bd7d44acc99e2f035e2654a3965d06d7f..990aaef2cbb72324824aa13a27ec443fe0684315 100644
--- a/benchmarks/zdc_lyso/config.yml
+++ b/benchmarks/zdc_lyso/config.yml
@@ -2,7 +2,7 @@ sim:zdc_lyso:
   extends: .det_benchmark
   stage: simulate
   script:
-    - snakemake --cache --cores 1 zdc_lyso_local
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 zdc_lyso_local
   retry:
     max: 2
     when:
@@ -16,5 +16,5 @@ collect_results:zdc_lyso:
   script:
     - ls -lrht
     - mv results{,_save}/ # move results directory out of the way to preserve it
-    - snakemake --cores 1 --delete-all-output zdc_lyso_local
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 --delete-all-output zdc_lyso_local
     - mv results{_save,}/
diff --git a/benchmarks/zdc_photon/config.yml b/benchmarks/zdc_photon/config.yml
index d62cef61dcb19b00bb9e0b12f65a6d1651f08910..9814792ae151a56d685477fb72b463a2054e6e98 100644
--- a/benchmarks/zdc_photon/config.yml
+++ b/benchmarks/zdc_photon/config.yml
@@ -12,7 +12,7 @@ sim:zdc_photon:
       - P: 200
       - P: 275
   script:
-    - snakemake --cores 5 sim_output/zdc_photon/epic_zdc_sipm_on_tile_only_rec_zdc_photon_${P}GeV_{0,1,2,3,4}.edm4eic.root
+    - snakemake $SNAKEMAKE_FLAGS --cores 5 sim_output/zdc_photon/epic_zdc_sipm_on_tile_only_rec_zdc_photon_${P}GeV_{0,1,2,3,4}.edm4eic.root
   retry:
     max: 2
     when:
diff --git a/benchmarks/zdc_pi0/config.yml b/benchmarks/zdc_pi0/config.yml
index f0b8993e843ec214865a968b06af0c019e23c3d2..0f9a68c4f52c4078921d28cb865a51c75e127bc6 100644
--- a/benchmarks/zdc_pi0/config.yml
+++ b/benchmarks/zdc_pi0/config.yml
@@ -9,7 +9,7 @@ sim:zdc_pi0:
       - P: 130
       - P: 160
   script:
-    - snakemake --cores 5 sim_output/zdc_pi0/epic_zdc_sipm_on_tile_only_rec_zdc_pi0_${P}GeV_{0,1,2,3,4}.edm4eic.root
+    - snakemake $SNAKEMAKE_FLAGS --cores 5 sim_output/zdc_pi0/epic_zdc_sipm_on_tile_only_rec_zdc_pi0_${P}GeV_{0,1,2,3,4}.edm4eic.root
   retry:
     max: 2
     when:
diff --git a/benchmarks/zdc_sigma/config.yml b/benchmarks/zdc_sigma/config.yml
index af204d4254a4ab0b48c1fa737fb33454f358bc41..17a84f392e6a5121f6a901c522aef110f8884d6f 100644
--- a/benchmarks/zdc_sigma/config.yml
+++ b/benchmarks/zdc_sigma/config.yml
@@ -12,7 +12,7 @@ sim:zdc_sigma:
       - P: 250
       - P: 275
   script:
-    - snakemake --cores 5 sim_output/zdc_sigma/epic_zdc_sipm_on_tile_only_rec_sigma_dec_${P}GeV_{0,1,2,3,4}.edm4eic.root
+    - snakemake $SNAKEMAKE_FLAGS --cores 5 sim_output/zdc_sigma/epic_zdc_sipm_on_tile_only_rec_sigma_dec_${P}GeV_{0,1,2,3,4}.edm4eic.root
   retry:
     max: 2
     when:
@@ -23,7 +23,7 @@ bench:zdc_sigma:
   stage: benchmarks
   needs: ["sim:zdc_sigma"]
   script:
-    - snakemake --cores 1 results/epic_zdc_sipm_on_tile_only/zdc_sigma
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 results/epic_zdc_sipm_on_tile_only/zdc_sigma
 
 collect_results:zdc_sigma:
   extends: .det_benchmark
@@ -32,5 +32,5 @@ collect_results:zdc_sigma:
   script:
     - ls -al
     - mv results{,_save}/ # move results directory out of the way to preserve it
-    - snakemake --cores 1 --delete-all-output results/epic_zdc_sipm_on_tile_only/zdc_sigma
+    - snakemake $SNAKEMAKE_FLAGS --cores 1 --delete-all-output results/epic_zdc_sipm_on_tile_only/zdc_sigma
     - mv results{_save,}/