diff --git a/scripts/tmfpython.sh b/scripts/tmfpython.sh
index beb8178..1b756a3 100755
--- a/scripts/tmfpython.sh
+++ b/scripts/tmfpython.sh
@@ -1,26 +1,26 @@
 #!/bin/bash
 
-#run with command: scripts/tmfpython.sh -p 1113 -t 2010 ...
-#p: project ID 
+#run with command: scripts/tmfpython.sh -i 'maps/aew85/projects' -o '/maps/aew85/tmf_pipe_out' -p 1113 -t 2010 ...
+#i: input dir - directory containing project shapefiles
+#o: output dir - directory containing pipeline outputs
+#p: project name/ID - must match name of shapefile
 #t: year of project start (t0)
 #e: evaluation year (default: 2022)
-#r: whether to run an ex-post evaluation and knit the results in an R notebook (true/false, default: false).
-#a: whether to run an ex-ante evaluation and knit the results in an R notebook (true/false, default: false).
+#v: verbose - whether to run an ex-post evaluation and knit the results in an R notebook (true/false, default: false).
 
 #NB running evaluations requires the evaluations code
 
 # Check which branch is currently checked out
-current_branch=$(git rev-parse --abbrev-ref HEAD)
+#current_branch=$(git rev-parse --abbrev-ref HEAD)
 
 set -e
 
 ############ DEFAULTS ###############
 
-input_dir="/maps/aew85/projects"
-output_dir="/maps/aew85/tmf_pipe_out"
+input_dir=""
+output_dir=""
 eval_year=2022
-ex_post=false
-ex_ante=false
+verbose=false
 
 #####################################
 
@@ -28,43 +28,46 @@ function display_help() {
     echo "Usage: $0 [options]"
     echo
     echo "Options:"
-    echo "  -p <project>        Project name"
+    echo "  -i <input_dir>      Input directory"
+    echo "  -o <output_dir>     Output directory"
+    echo "  -p <proj>           Project name"
     echo "  -t <t0>             Start year"
     echo "  -e <year>           Evaluation year"
-    echo "  -r <ex_post>        Knit ex post evaluation? (true/false)"
-    echo "  -a <ex_ante>        Knit ex ante evaluation? (true/false)"
+    echo "  -v <verbose>        Knit ex post evaluation as .Rmd? (true/false)"
     echo "  -h                  Display this help message"
-    echo
     echo "Example:"
     echo "  $0 -p 'gola' -t 2012 -e 2021 -r true -a true"
 }
 
 # Parse arguments
-while getopts "p:t:e:r:a:h" flag
+while getopts "i:o:p:t:e:v:h" flag
 do
     case "${flag}" in
+        p) input_dir=${OPTARG};;
+        t) output_dir=${OPTARG};;
         p) proj=${OPTARG};;
         t) t0=${OPTARG};;
         e) eval_year=${OPTARG};;
-        r) ex_post=${OPTARG};;
+        r) verbose=${OPTARG};;
         a) ex_ante=${OPTARG};;
         h) display_help; exit 0;;
         *) echo "Invalid option: -${OPTARG}" >&2; display_help; exit 1;;
     esac
 done
 
+echo "Input directory: $input_dir"
+echo "Output directory: $output_dir"
 echo "Project: $proj"
 echo "t0: $t0"
 echo "Evaluation year: $eval_year"
-echo "Ex-post evaluation: $ex_post"
-echo "Ex-ante evaluation: $ex_ante"
+echo "Ex-post evaluation: $verbose"
 
 if [ $# -eq 0 ]; then
     display_help
     exit 1
 fi
 
-# Make project output directory
+# Make project output folder
 mkdir -p "${output_dir}/${proj}"
 echo "--Folder created.--"
 
@@ -182,46 +185,27 @@ echo "--Set M created.--"
 
 #Matching: find pairs
 tmfpython3 -m methods.matching.find_pairs \
-    --k "${output_dir}/${proj}/k.parquet" \
-    --m "${output_dir}/${proj}/matches.parquet" \
-    --start_year "$t0" \
-    --output "${output_dir}/${proj}/pairs" \
-    --seed 42 \
-    -j 1
-    echo "--Pairs matched.--"
+--k "${output_dir}/${proj}/k.parquet" \
+--m "${output_dir}/${proj}/matches.parquet" \
+--start_year "$t0" \
+--output "${output_dir}/${proj}/pairs" \
+--seed 42 \
+-j 1 
+echo "--Pairs matched.--"
 
 #Calculate additionality
-if [ "$current_branch" == "mwd-check-stopping-criteria" ]; then
-    tmfpython3 -m methods.outputs.calculate_additionality \
-    --project "${input_dir}/${proj}.geojson" \
-    --project_start "$t0" \
-    --evaluation_year "$eval_year" \
-    --density "${output_dir}/${proj}/carbon-density.csv" \
-    --matches "${output_dir}/${proj}/pairs" \
-    --output "${output_dir}/${proj}/additionality.csv" \
-    --stopping "${output_dir}/${proj}/stopping.csv"
-    echo "--Additionality and stopping criteria calculated.--"
-    else
-    tmfpython3 -m methods.outputs.calculate_additionality \
-    --project "${input_dir}/${proj}.geojson" \
-    --project_start "$t0" \
-    --evaluation_year "$eval_year" \
-    --density "${output_dir}/${proj}/carbon-density.csv" \
-    --matches "${output_dir}/${proj}/pairs" \
-    --output "${output_dir}/${proj}/additionality.csv"
-    echo "--Additionality calculated.--"
-fi
+tmfpython3 -m methods.outputs.calculate_additionality \
+--project "${input_dir}/${proj}.geojson" \
+--project_start "$t0" \
+--evaluation_year "$eval_year" \
+--density "${output_dir}/${proj}/carbon-density.csv" \
+--matches "${output_dir}/${proj}/pairs" \
+--output "${output_dir}/${proj}/additionality.csv"
+echo "--Additionality calculated.--"
 
 # Run ex post evaluation
-if [ "$ex_post" == "true" ]; then
-evaluations_dir="~/evaluations"
-ep_output_file="${evaluations_dir}/${proj}_ex_post_evaluation.html"
-Rscript -e "rmarkdown::render(input='~/evaluations/R/ex_post_evaluation_template.Rmd',output_file='${ep_output_file}',params=list(proj='${proj}',t0='${t0}',eval_year='${eval_year}',input_dir='${input_dir}',output_dir='${output_dir}',evaluations_dir='${evaluations_dir}'))"
+if [ "$verbose" == "true" ]; then
+    evaluations_dir="~/evaluations"
+    ep_output_file="${evaluations_dir}/${proj}_ex_post_evaluation.html"
+    Rscript -e "rmarkdown::render(input='~/evaluations/R/ex_post_evaluation_template.Rmd',output_file='${ep_output_file}',params=list(proj='${proj}',t0='${t0}',eval_year='${eval_year}',input_dir='${input_dir}',output_dir='${output_dir}'))"
 fi
-
-# Run ex-ante evaluation
-if [ "$ex_ante" == "true" ]; then
-evaluations_dir="~/evaluations"
-ea_output_file="${evaluations_dir}/${proj}_ex_ante_evaluation.html"
-Rscript -e "rmarkdown::render(input='~/evaluations/R/ex_ante_evaluation_template.Rmd',output_file='${ea_output_file}',params=list(proj='${proj}',t0='${t0}',eval_year='${eval_year}',input_dir='${input_dir}',output_dir='${output_dir}',evaluations_dir='${evaluations_dir}'))"
-fi
\ No newline at end of file