diff --git a/DIMS/GenerateBreaks.R b/DIMS/GenerateBreaks.R
index e8beffb8..007d5ab7 100644
--- a/DIMS/GenerateBreaks.R
+++ b/DIMS/GenerateBreaks.R
@@ -5,19 +5,56 @@ suppressPackageStartupMessages(library("xcms"))
 cmd_args <- commandArgs(trailingOnly = TRUE)
 
 filepath <- cmd_args[1]
-trim <- as.numeric(cmd_args[2])
-resol <- as.numeric(cmd_args[3])
+outdir <- cmd_args[2]
+trim <- as.numeric(cmd_args[3])
+resol <- as.numeric(cmd_args[4])
+
+# initialize
+trim_left_pos <- NULL
+trim_right_pos <- NULL
+trim_left_neg <- NULL
+trim_right_neg <- NULL
+breaks_fwhm <- NULL
+breaks_fwhm_avg <- NULL
+bins <- NULL
 
 # read in mzML file
 raw_data <- suppressMessages(xcms::xcmsRaw(filepath))
 
-# get trim parameters and save them to file
-get_trim_parameters(raw_data@scantime, raw_data@polarity, trim)
+# Get time values for positive and negative scans
+pos_times <- raw_data@scantime[raw_data@polarity == "positive"]
+neg_times <- raw_data@scantime[raw_data@polarity == "negative"]
+
+# trim (remove) scans at the start and end for positive
+trim_left_pos  <- round(pos_times[length(pos_times) * (trim * 1.5)]) # 15% aan het begin
+trim_right_pos <- round(pos_times[length(pos_times) * (1 - (trim * 0.5))]) # 5% aan het eind
 
-# create breaks of bins for intensities. Bin size is a function of fwhm which is a function of m/z
-get_breaks_for_bins(raw_data$mzrange, resol)
+# trim (remove) scans at the start and end for negative
+trim_left_neg  <- round(neg_times[length(neg_times) * trim])
+trim_right_neg <- round(neg_times[length(neg_times) * (1 - trim)])
 
-# Determine maximum m/z and save to file
+# Mass range m/z
+low_mz  <- raw_data@mzrange[1]
 high_mz <- raw_data@mzrange[2]
-save(high_mz, file = "highest_mz.RData")
 
+# determine number of segments (bins)
+nr_segments <- 2 * (high_mz - low_mz)
+segment <- seq(from = low_mz, to = high_mz, length.out = nr_segments + 1)
+
+# determine start and end of each bin.
+for (i in 1:nr_segments) {
+  start_segment <- segment[i]
+  end_segment <- segment[i+1]
+  resol_mz <- resol * (1 / sqrt(2) ^ (log2(start_segment / 200)))
+  fwhm_segment <- start_segment / resol_mz
+  breaks_fwhm <- c(breaks_fwhm, seq(from = (start_segment + fwhm_segment), to = end_segment, by = 0.2 * fwhm_segment))
+  # average the m/z instead of start value
+  range <- seq(from = (start_segment + fwhm_segment), to = end_segment, by = 0.2 * fwhm_segment)
+  delta_mz <- range[2] - range[1]
+  breaks_fwhm_avg <- c(breaks_fwhm_avg, range + 0.5 * delta_mz)
+}
+
+# generate output file
+save(breaks_fwhm, breaks_fwhm_avg, file = "breaks.fwhm.RData")
+save(trim_left_pos, trim_right_pos, trim_left_neg, trim_right_neg, file = "trim_params.RData")
+save(high_mz, file = "highest_mz.RData")
diff --git a/DIMS/GenerateBreaks.nf b/DIMS/GenerateBreaks.nf
index e2dc2d46..c486010d 100644
--- a/DIMS/GenerateBreaks.nf
+++ b/DIMS/GenerateBreaks.nf
@@ -7,6 +7,7 @@ process GenerateBreaks {
     input:
        tuple(val(file_id), path(mzML_file))
 
+
     output:
        path('breaks.fwhm.RData'), emit: breaks
        path('trim_params.RData'), emit: trim_params
@@ -14,6 +15,6 @@ process GenerateBreaks {
 
     script:
         """
-        Rscript ${baseDir}/CustomModules/DIMS/GenerateBreaks.R $mzML_file $params.trim $params.resolution 
+        Rscript ${baseDir}/CustomModules/DIMS/GenerateBreaks.R $mzML_file ./ $params.trim $params.resolution 
         """
 }
diff --git a/DIMS/MakeInit.R b/DIMS/MakeInit.R
new file mode 100644
index 00000000..9ff22623
--- /dev/null
+++ b/DIMS/MakeInit.R
@@ -0,0 +1,29 @@
+# define parameters
+args <- commandArgs(trailingOnly = TRUE)
+
+sample_sheet <- read.csv(args[1], sep = "\t")
+nr_replicates <- as.numeric(args[2])
+
+sample_names <- trimws(as.vector(unlist(sample_sheet[1])))
+nr_sample_groups <- length(sample_names) / nr_replicates
+group_names <- trimws(as.vector(unlist(sample_sheet[2])))
+group_names <- gsub("[^-.[:alnum:]]", "_", group_names)
+group_names_unique <- unique(group_names)
+
+# generate the replication pattern
+repl_pattern <- c()
+for (sample_group in 1:nr_sample_groups) {
+  replicates_persample <- c()
+  for (repl in nr_replicates:1) {
+    index <- ((sample_group * nr_replicates) - repl) + 1
+    replicates_persample <- c(replicates_persample, sample_names[index])
+  }
+  repl_pattern <- c(repl_pattern, list(replicates_persample))
+}
+
+names(repl_pattern) <- group_names_unique
+
+# preview the replication pattern
+print(tail(repl_pattern))
+
+save(repl_pattern, file = "init.RData")
diff --git a/DIMS/MakeInit.nf b/DIMS/MakeInit.nf
new file mode 100644
index 00000000..7aae0e46
--- /dev/null
+++ b/DIMS/MakeInit.nf
@@ -0,0 +1,18 @@
+process MakeInit {
+    tag "DIMS MakeInit"
+    label 'MakeInit'
+    container = 'docker://umcugenbioinf/dims:1.3'
+    shell = ['/bin/bash', '-euo', 'pipefail']
+
+    input:
+       path(samplesheet) 
+       val(nr_replicates)
+
+    output:
+       path('init.RData')
+
+    script:
+        """
+        Rscript ${baseDir}/CustomModules/DIMS/MakeInit.R $samplesheet $nr_replicates 
+        """
+}
diff --git a/DIMS/ParseSamplesheet.R b/DIMS/ParseSamplesheet.R
deleted file mode 100644
index 806486fb..00000000
--- a/DIMS/ParseSamplesheet.R
+++ /dev/null
@@ -1,19 +0,0 @@
-# define parameters
-args <- commandArgs(trailingOnly = TRUE)
-
-sample_sheet <- as.data.frame(read.csv(args[1], sep = "\t"))
-preprocessing_scripts_dir <- args[2]
-
-# load in function script
-source(paste0(preprocessing_scripts_dir, "parse_samplesheet_functions.R"))
-
-# generate the replication pattern
-repl_pattern <- generate_repl_pattern(sample_sheet)
-
-# write the replication pattern to text file for troubleshooting purposes
-sink("replication_pattern.txt")
-print(repl_pattern)
-sink()
-
-# save replication pattern to file
-save(repl_pattern, file = "init.RData")
diff --git a/DIMS/ParseSamplesheet.nf b/DIMS/ParseSamplesheet.nf
deleted file mode 100644
index e0fc055b..00000000
--- a/DIMS/ParseSamplesheet.nf
+++ /dev/null
@@ -1,18 +0,0 @@
-process ParseSamplesheet {
-    tag "DIMS ParseSamplesheet"
-    label 'ParseSamplesheet'
-    container = 'docker://umcugenbioinf/dims:1.3'
-
-    input:
-       path(samplesheet) 
-       val(preprocessing_scripts_dir)
-
-    output:
-       path('init.RData'), emit: rdata_file
-       path('replication_pattern.txt'), emit: repl_pattern_txtfile
-
-    script:
-        """
-        Rscript ${baseDir}/CustomModules/DIMS/ParseSamplesheet.R $samplesheet $preprocessing_scripts_dir
-        """
-}
diff --git a/DIMS/preprocessing/generate_breaks_functions.R b/DIMS/preprocessing/generate_breaks_functions.R
deleted file mode 100644
index 9fc84125..00000000
--- a/DIMS/preprocessing/generate_breaks_functions.R
+++ /dev/null
@@ -1,59 +0,0 @@
-# GenerateBreaks functions
-get_trim_parameters <- function(scantimes, polarities, trim = 0.1) {
-  #' determine the scans per scanmode which are trimmed off; save trim parameters to file
-  #'
-  #' @param scantimes: vector of scan times in seconds 
-  #' @param polarities: vector of polarities (positive or negative)
-  #' @param trim: value for fraction of scans which are to be discarded (float)
-  
-  # Get time values for positive and negative scans
-  pos_times <- scantimes[polarities == "positive"]
-  neg_times <- scantimes[polarities == "negative"]
-  
-  # trim: remove scans at the start and end for positive
-  trim_left_pos  <- round(pos_times[length(pos_times) * (trim * 1.5)])
-  trim_right_pos <- round(pos_times[length(pos_times) * (1 - (trim * 0.5))])
-  
-  # trim: remove scans at the start and end for negative
-  trim_left_neg  <- round(neg_times[length(neg_times) * trim])
-  trim_right_neg <- round(neg_times[length(neg_times) * (1 - trim)])
-  
-  # save trim parameters to file
-  save(trim_left_pos, trim_right_pos, trim_left_neg, trim_right_neg, file = "trim_params.RData")
-}
-
-get_breaks_for_bins <- function(mzrange, resol = 140000) {
-  #' create a vector with the breaks in m/z of bins for intensities
-  #'
-  #' @param mzrange: vector of minimum and maximum m/z values (integeers)
-  #' @param resol: value for resolution (integer)
-  
-  # initialize
-  breaks_fwhm <- NULL
-  breaks_fwhm_avg <- NULL
-  
-  # determine number of segments used to create bins
-  nr_segments <- 2 * (mzrange[2] - mzrange[1])
-  segments <- seq(from = mzrange[1], to = mzrange[2], length.out = nr_segments + 1)
-  
-  # determine start and end of each bin. fwhm (width of peaks) is assumed to be constant within a segment
-  for (segment_index in 1:nr_segments) {
-    start_segment <- segments[segment_index]
-    end_segment <- segments[segment_index + 1]
-    # determine resolution at given m/z value
-    resol_mz <- resol * (1 / sqrt(2) ^ (log2(start_segment / 200)))
-    # determine fwhm (full width at half maximum) of the peaks in this segment
-    fwhm_segment <- start_segment / resol_mz
-    # determine the breaks within this segment
-    breaks_segment <- seq(from = (start_segment + fwhm_segment), to = end_segment, by = 0.2 * fwhm_segment)
-    # add breaks for this segment to vector with all breaks
-    breaks_fwhm <- c(breaks_fwhm, seq(from = (start_segment + fwhm_segment), to = end_segment, by = 0.2 * fwhm_segment))
-    # get a vector of average m/z instead of start value
-    delta_mz <- breaks_segment[2] - breaks_segment[1]
-    avg_breaks_segment <- breaks_segment + 0.5 * delta_mz
-    breaks_fwhm_avg <- c(breaks_fwhm_avg, avg_breaks_segment)
-  }
-  
-  # save breaks to file
-  save(breaks_fwhm, breaks_fwhm_avg, file = "breaks.fwhm.RData")
-}
diff --git a/DIMS/preprocessing/parse_samplesheet_functions.R b/DIMS/preprocessing/parse_samplesheet_functions.R
deleted file mode 100644
index 9107ba6a..00000000
--- a/DIMS/preprocessing/parse_samplesheet_functions.R
+++ /dev/null
@@ -1,30 +0,0 @@
-# function for parse_samplesheet
-
-#' Generate replication pattern list based on information in sample_sheet
-#'
-#' @param sample_sheet: matrix of file names and sample names
-#'
-#' @return ints_sorted: list of sample names with corresponding file names (technical replicates)
-generate_repl_pattern <- function(sample_sheet) {
-  # get the file name and sample name columns from the samplesheet
-  file_name_col <- grep("File_Name|File Name", colnames(sample_sheet), ignore.case = TRUE)
-  sample_name_col <- grep("Sample_Name|Sample Name", colnames(sample_sheet), ignore.case = TRUE)
-  # get the unique sample names from the samplesheet
-    sample_names <- sample_sheet[sample_name_col] |>
-    unlist() |>
-    as.vector() |>
-    trimws() |>
-    unique() |>
-    sort()
-  # remove all characters from sample_names which are not letters, numbers, hyphens and periods
-  sample_names <- gsub("[^-.[:alnum:]]", "_", sample_names)
-
-  # create replication pattern (which technical replicates belong to which sample)
-  repl_pattern <- split(
-    sample_sheet[[file_name_col]],
-    sample_sheet[[sample_name_col]]
-  )
-
-  return(repl_pattern)
-}
-
diff --git a/DIMS/tests/testthat/fixtures/test_breaks.fwhm.RData b/DIMS/tests/testthat/fixtures/test_breaks.fwhm.RData
deleted file mode 100644
index 699281d5..00000000
Binary files a/DIMS/tests/testthat/fixtures/test_breaks.fwhm.RData and /dev/null differ
diff --git a/DIMS/tests/testthat/fixtures/test_trim_params.RData b/DIMS/tests/testthat/fixtures/test_trim_params.RData
deleted file mode 100644
index f9370f55..00000000
Binary files a/DIMS/tests/testthat/fixtures/test_trim_params.RData and /dev/null differ
diff --git a/DIMS/tests/testthat/parse_samplesheet_functions.R b/DIMS/tests/testthat/parse_samplesheet_functions.R
deleted file mode 100644
index 8e467967..00000000
--- a/DIMS/tests/testthat/parse_samplesheet_functions.R
+++ /dev/null
@@ -1,24 +0,0 @@
-# unit tests for ParseSamplesheet
-# function: generate_repl_pattern
-
-# source all functions for ParseSamplesheet
-source("../../preprocessing/parse_samplesheet_functions.R")
-
-# test generate_repl_pattern
-testthat::test_that("replication pattern is correctly generated", {
-  # create sample sheet tot test on:
-  test_file_names <- paste0(rep("RES_20260101_", 6), sprintf("%03d", 1:6))
-  test_sample_names <- sort(rep(c("C1", "P2", "P3"), 2))
-  test_sample_sheet <- as.data.frame(cbind(File_Name = test_file_names, Sample_Name = test_sample_names))
-
-  # test that a list of length 3 is generated
-  expect_length(generate_repl_pattern(test_sample_sheet), 3)
-  # test list names
-  expect_equal(names(generate_repl_pattern(test_sample_sheet)), unique(test_sample_names), TRUE)
-  
-  # test what happens if any sample name is used twice
-  test_sample_names <- gsub("P3", "P2", test_sample_names)
-  test_sample_sheet <- as.data.frame(cbind(File_Name = test_file_names, Sample_Name = test_sample_names))
-  expect_length(generate_repl_pattern(test_sample_sheet), 2)
-  expect_length(generate_repl_pattern(test_sample_sheet)$P2, 4)
-})
diff --git a/DIMS/tests/testthat/test_generate_breaks.R b/DIMS/tests/testthat/test_generate_breaks.R
deleted file mode 100644
index bd383733..00000000
--- a/DIMS/tests/testthat/test_generate_breaks.R
+++ /dev/null
@@ -1,54 +0,0 @@
-# unit tests for GenerateBreaks
-# functions: get_trim_parameters and get_breaks_for_bins
-
-# source all functions for GenerateBreaks
-source("../../preprocessing/generate_breaks_functions.R")
-
-# test get_trim_parameters
-testthat::test_that("trim parameters are correctly calculated", {
-  # create list of scan times to test on:
-  test_scantimes <- seq(0, 100, length = 168)
-  test_polarities <- c(rep("positive", 84), rep("negative", 84))
-  test_trim <- 0.1
-
-  # test that the function produces no output except trim_params.RData file
-  expect_silent(get_trim_parameters(test_scantimes, test_polarities, test_trim))
-  expect_true(file.exists("./trim_params.RData"))
-
-  # test the parameters in the output RData file
-  load("./trim_params.RData")
-  test_trim_left_pos  <- trim_left_pos
-  test_trim_left_neg  <- trim_left_neg
-  test_trim_right_pos <- trim_right_pos
-  test_trim_right_neg <- trim_right_neg
-  rm(trim_left_pos, trim_left_neg, trim_right_pos, trim_right_neg)
-
-  # load previously stored values from fixtures
-  load("fixtures/test_trim_params.RData")
-  expect_equal(test_trim_left_pos,  trim_left_pos)
-  expect_equal(test_trim_left_neg,  trim_left_neg)
-  expect_equal(test_trim_right_pos, trim_right_pos)
-  expect_equal(test_trim_right_neg, trim_right_neg)
-})
-
-# test get_breaks_for_bins
-testthat::test_that("breaks are correctly calculated", {
-  # create list of scan times to test on:
-  test_mzrange <- c(300, 400)
-  test_resol <- 140000
-  
-  # test that the function produces no output except breaks.fwhm.RData file
-  expect_silent(get_breaks_for_bins(test_mzrange, test_resol))
-  expect_true(file.exists("./breaks.fwhm.RData"))
-  
-  # test the vectors in the output RData file
-  load("./breaks.fwhm.RData")
-  test_breaks_fwhm <- breaks_fwhm
-  test_breaks_fwhm_avg <- breaks_fwhm_avg
-  rm(breaks_fwhm, breaks_fwhm_avg)
-
-  # load breaks from fixtures and compare vectors
-  load("fixtures/test_breaks.fwhm.RData")
-  expect_equal(test_breaks_fwhm, breaks_fwhm)
-  expect_equal(test_breaks_fwhm_avg, breaks_fwhm_avg)
-})