diff --git a/DIMS/AssignToBins.R b/DIMS/AssignToBins.R
index 49d4528..7028b49 100644
--- a/DIMS/AssignToBins.R
+++ b/DIMS/AssignToBins.R
@@ -1,19 +1,22 @@
 # load required packages
+library("argparse")
 suppressPackageStartupMessages(library("xcms"))
 
-# define parameters
-cmd_args <- commandArgs(trailingOnly = TRUE)
+parser <- ArgumentParser(description = "AssignToBins")
 
-mzml_filepath <- cmd_args[1]
-breaks_filepath <- cmd_args[2]
-resol <- as.numeric(cmd_args[3])
+parser$add_argument("--mzML_filepath", dest = "mzml_filepath",
+                    help = "File path for the mzML file", required = TRUE)
+parser$add_argument("--breaks_filepath", dest = "breaks_filepath",
+                    help = "File path for the breaks RData file", required = TRUE)
+
+args <- parser$parse_args()
 
 # load breaks_file: contains breaks_fwhm, breaks_fwhm_avg,
 # trim_left_neg, trim_left_pos, trim_right_neg & trim_right_pos
-load(breaks_filepath)
+load(args$breaks_filepath)
 
 # get sample name
-techrep_name <- sub("\\..*$", "", basename(mzml_filepath))
+techrep_name <- sub("\\..*$", "", basename(args$mzml_filepath))
 
 options(digits = 16)
 
@@ -26,7 +29,7 @@ neg_bins <- bins
 dims_thresh <- 100
 
 # read in the data for 1 sample
-raw_data <- suppressMessages(xcms::xcmsRaw(mzml_filepath))
+raw_data <- suppressMessages(xcms::xcmsRaw(args$mzml_filepath))
 
 # Generate a matrix with retention times and intensities
 raw_data_matrix <- xcms::rawMat(raw_data)
@@ -41,13 +44,13 @@ neg_times_trimmed <- neg_times[neg_times > trim_left_neg & neg_times < trim_righ
 # get TIC intensities for areas between trim_left and trim_right
 tic_intensity_persample <- cbind(raw_data@scantime, raw_data@tic)
 colnames(tic_intensity_persample) <- c("retention_time", "tic_intensity")
-tic_intensity_pos <- tic_intensity_persample[tic_intensity_persample[ , "retention_time"] > min(pos_times_trimmed) &
-                                             tic_intensity_persample[ , "retention_time"] < max(pos_times_trimmed), ]
-tic_intensity_neg <- tic_intensity_persample[tic_intensity_persample[ , "retention_time"] > min(neg_times_trimmed) &
-                                             tic_intensity_persample[ , "retention_time"] < max(neg_times_trimmed), ]
+tic_intensity_pos <- tic_intensity_persample[tic_intensity_persample[, "retention_time"] > min(pos_times_trimmed) &
+                                               tic_intensity_persample[, "retention_time"] < max(pos_times_trimmed), ]
+tic_intensity_neg <- tic_intensity_persample[tic_intensity_persample[, "retention_time"] > min(neg_times_trimmed) &
+                                               tic_intensity_persample[, "retention_time"] < max(neg_times_trimmed), ]
 # calculate weighted mean of intensities for pos and neg separately
-mean_pos <- weighted.mean(tic_intensity_pos[ , "tic_intensity"], tic_intensity_pos[ , "tic_intensity"])
-mean_neg <- weighted.mean(tic_intensity_neg[ , "tic_intensity"], tic_intensity_neg[ , "tic_intensity"])
+mean_pos <- weighted.mean(tic_intensity_pos[, "tic_intensity"], tic_intensity_pos[, "tic_intensity"])
+mean_neg <- weighted.mean(tic_intensity_neg[, "tic_intensity"], tic_intensity_neg[, "tic_intensity"])
 # intensity per scan should be at least 80% of weighted mean
 dims_thresh_pos <- 0.8 * mean_pos
 dims_thresh_neg <- 0.8 * mean_neg
@@ -67,17 +70,17 @@ neg_raw_data_matrix <- raw_data_matrix[neg_index, ]
 
 # Get index for binning intensity values
 bin_indices_pos <- cut(
-  pos_raw_data_matrix[, "mz"], 
+  pos_raw_data_matrix[, "mz"],
   breaks_fwhm,
-  include.lowest = TRUE, 
-  right = TRUE, 
+  include.lowest = TRUE,
+  right = TRUE,
   labels = FALSE
 )
 bin_indices_neg <- cut(
-  neg_raw_data_matrix[, "mz"], 
-  breaks_fwhm, 
-  include.lowest = TRUE, 
-  right = TRUE, 
+  neg_raw_data_matrix[, "mz"],
+  breaks_fwhm,
+  include.lowest = TRUE,
+  right = TRUE,
   labels = FALSE
 )
 
diff --git a/DIMS/AssignToBins.nf b/DIMS/AssignToBins.nf
index d0a7098..df3b089 100644
--- a/DIMS/AssignToBins.nf
+++ b/DIMS/AssignToBins.nf
@@ -1,7 +1,7 @@
 process AssignToBins {
     tag "DIMS AssignToBins ${file_id}"
     label 'AssignToBins'
-    container = 'docker://umcugenbioinf/dims:1.3'
+    container = 'docker://umcugenbioinf/dims:1.4'
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
@@ -13,7 +13,9 @@ process AssignToBins {
 
     script:
         """
-        Rscript ${baseDir}/CustomModules/DIMS/AssignToBins.R $mzML_file $breaks_file $params.resolution
+        Rscript ${baseDir}/CustomModules/DIMS/AssignToBins.R \\
+            --mzML_filepath $mzML_file \\
+            --breaks_filepath $breaks_file
         """
 }
 
diff --git a/DIMS/AverageTechReplicates.R b/DIMS/AverageTechReplicates.R
index 1c727d1..6376339 100644
--- a/DIMS/AverageTechReplicates.R
+++ b/DIMS/AverageTechReplicates.R
@@ -1,28 +1,37 @@
 # adapted from 3-AverageTechReplicates.R
 
 # load packages
+library("argparse")
 library("ggplot2")
 library("gridExtra")
 
-# define parameters
-cmd_args <- commandArgs(trailingOnly = TRUE)
+parser <- ArgumentParser(description = "AverageTechReplicates")
 
-init_file <- cmd_args[1]
-nr_replicates <- as.numeric(cmd_args[2])
-run_name <- cmd_args[3]
-dims_matrix <- cmd_args[4]
-highest_mz_file <- cmd_args[5]
-highest_mz <- get(load(highest_mz_file))
-breaks_filepath <- cmd_args[6]
-thresh2remove <- as.numeric(cmd_args[7])
+parser$add_argument("--init_filepath", dest = "init_file",
+                    help = "File path for the init RData file", required = TRUE)
+parser$add_argument("-n", "--nr_replicates", dest = "nr_replicates", type = "integer",
+                    help = "Number of replicates", required = TRUE)
+parser$add_argument("--run_name", dest = "run_name",
+                    help = "The run name/analysis ID", required = TRUE)
+parser$add_argument("--matrix", dest = "dims_matrix",
+                    help = "The matrix used, e.g. Plasma, Research, ...")
+parser$add_argument("--highest_mz_file", dest = "highest_mz_file",
+                    help = "File path for the highest Mz RData file", required = TRUE)
+parser$add_argument("--breaks_filepath", dest = "breaks_filepath",
+                    help = "File path for the breaks RData file", required = TRUE)
+
+args <- parser$parse_args()
+
+highest_mz <- get(load(args$highest_mz_file))
+thresh2remove <- 1000000000
 
 remove_from_repl_pattern <- function(bad_samples, repl_pattern, nr_replicates) {
   # collect list of samples to remove from replication pattern
   remove_from_group <- NULL
-  for (sample_nr in 1:length(repl_pattern)){
+  for (sample_nr in seq_along(repl_pattern)){
     repl_pattern_1sample <- repl_pattern[[sample_nr]]
     remove <- NULL
-    for (file_nr in 1:length(repl_pattern_1sample)) {
+    for (file_nr in seq_along(repl_pattern_1sample)) {
       if (repl_pattern_1sample[file_nr] %in% bad_samples) {
         remove <- c(remove, file_nr)
       }
@@ -41,11 +50,11 @@ remove_from_repl_pattern <- function(bad_samples, repl_pattern, nr_replicates) {
 }
 
 # load init_file: contains repl_pattern
-load(init_file)
+load(args$init_file)
 
 # load breaks_file: contains breaks_fwhm, breaks_fwhm_avg,
 # trim_left_neg, trim_left_pos, trim_right_neg & trim_right_pos
-load(breaks_filepath)
+load(args$breaks_filepath)
 
 # lower the threshold for non Plasma matrices
 if (dims_matrix != "Plasma") {
@@ -64,7 +73,7 @@ if (highest_mz > 700) {
 remove_neg <- NULL
 remove_pos <- NULL
 cat("Pklist sum threshold to remove technical replicate:", thresh2remove, "\n")
-for (sample_nr in 1:length(repl_pattern)) {
+for (sample_nr in seq_along(repl_pattern)) {
   tech_reps <- as.vector(unlist(repl_pattern[sample_nr]))
   tech_reps_array_pos <- NULL
   tech_reps_array_neg <- NULL
@@ -72,7 +81,7 @@ for (sample_nr in 1:length(repl_pattern)) {
   sum_pos <- 0
   nr_pos <- 0
   nr_neg <- 0
-  for (file_nr in 1:length(tech_reps)) {
+  for (file_nr in seq_along(tech_reps)) {
     load(paste(tech_reps[file_nr], ".RData", sep = ""))
     cat("\n\nParsing", tech_reps[file_nr])
     # negative scanmode
@@ -96,7 +105,7 @@ for (sample_nr in 1:length(repl_pattern)) {
     }
     tech_reps_array_pos <- cbind(tech_reps_array_pos, peak_list$pos)
   }
-  # save to file  
+  # save to file
   if (nr_neg != 0) {
     sum_neg[, 1] <- sum_neg[, 1] / nr_neg
     colnames(sum_neg) <- names(repl_pattern)[sample_nr]
@@ -109,25 +118,25 @@ for (sample_nr in 1:length(repl_pattern)) {
   }
 }
 
-pattern_list <- remove_from_repl_pattern(remove_neg, repl_pattern, nr_replicates)
+pattern_list <- remove_from_repl_pattern(remove_neg, repl_pattern, args$nr_replicates)
 repl_pattern_filtered <- pattern_list$pattern
 save(repl_pattern_filtered, file = "negative_repl_pattern.RData")
 write.table(
-  remove_neg, 
-  file = "miss_infusions_negative.txt", 
-  row.names = FALSE, 
-  col.names = FALSE, 
+  remove_neg,
+  file = "miss_infusions_negative.txt",
+  row.names = FALSE,
+  col.names = FALSE,
   sep = "\t"
 )
 
-pattern_list <- remove_from_repl_pattern(remove_pos, repl_pattern, nr_replicates)
+pattern_list <- remove_from_repl_pattern(remove_pos, repl_pattern, args$nr_replicates)
 repl_pattern_filtered <- pattern_list$pattern
 save(repl_pattern_filtered, file = "positive_repl_pattern.RData")
 write.table(
-  remove_pos, 
-  file = "miss_infusions_positive.txt", 
-  row.names = FALSE, 
-  col.names = FALSE, 
+  remove_pos,
+  file = "miss_infusions_positive.txt",
+  row.names = FALSE,
+  col.names = FALSE,
   sep = "\t"
 )
 
@@ -150,10 +159,10 @@ for (file in tic_files) {
 # create a list with information for all TIC plots
 tic_plot_list <- list()
 plot_nr <-  0
-for (sample_nr in c(1:length(repl_pattern))) {
+for (sample_nr in seq_along(repl_pattern)) {
   tech_reps <- as.vector(unlist(repl_pattern[sample_nr]))
   sample_name <- names(repl_pattern)[sample_nr]
-  for (file_nr in 1:length(tech_reps)) {
+  for (file_nr in seq_along(tech_reps)) {
     plot_nr <- plot_nr + 1
     # read file with retention time, intensity and dims_threshold values
     repl1_nr <- read.table(paste0(tech_reps[file_nr], "_TIC.txt"))
@@ -163,7 +172,7 @@ for (sample_nr in c(1:length(repl_pattern))) {
     # for replicates with bad TIC, determine what color the border of the plot should be
     bad_color_pos <- tech_reps[file_nr] %in% remove_pos
     bad_color_neg <- tech_reps[file_nr] %in% remove_neg
-    if (bad_color_neg & bad_color_pos) {
+    if (bad_color_neg && bad_color_pos) {
       plot_color <- "#F8766D"
     } else if (bad_color_pos) {
       plot_color <- "#ED8141"
@@ -191,19 +200,19 @@ for (sample_nr in c(1:length(repl_pattern))) {
 }
 
 # create a layout matrix dependent on number of replicates
-layout <- matrix(1:(10 * nr_replicates), 10, nr_replicates, TRUE)
+layout <- matrix(1:(10 * args$nr_replicates), 10, args$nr_replicates, TRUE)
 # put TIC plots in matrix
 tic_plot_pdf <- marrangeGrob(
   grobs = tic_plot_list,
-  nrow = 10, ncol = nr_replicates,
+  nrow = 10, ncol = args$nr_replicates,
   layout_matrix = layout,
   top = quote(paste(
-    "TICs of run", run_name,
+    "TICs of run", args$run_name,
     " \n colors: red = both modes misinjection, orange = pos mode misinjection, purple = neg mode misinjection \n ",
     g, "/", npages
   ))
 )
 
 # save to file
-ggsave(filename = paste0(run_name, "_TICplots.pdf"),
+ggsave(filename = paste0(args$run_name, "_TICplots.pdf"),
        tic_plot_pdf, width = 21, height = 29.7, units = "cm")
diff --git a/DIMS/AverageTechReplicates.nf b/DIMS/AverageTechReplicates.nf
index f03d553..12606cf 100644
--- a/DIMS/AverageTechReplicates.nf
+++ b/DIMS/AverageTechReplicates.nf
@@ -1,7 +1,7 @@
 process AverageTechReplicates {
     tag "DIMS AverageTechReplicates"
     label 'AverageTechReplicates'
-    container = 'docker://umcugenbioinf/dims:1.3'
+    container = 'docker://umcugenbioinf/dims:1.4'
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
@@ -23,13 +23,13 @@ process AverageTechReplicates {
 
     script:
         """
-        Rscript ${baseDir}/CustomModules/DIMS/AverageTechReplicates.R $init_file \
-                                                                      $params.nr_replicates \
-                                                                      $analysis_id \
-                                                                      $matrix \
-                                                                      $highest_mz_file \
-                                                                      $breaks_file \
-                                                                      $params.threshold_tics
+        Rscript ${baseDir}/CustomModules/DIMS/AverageTechReplicates.R \\
+            --init_filepath $init_file \\
+            --nr_replicates $params.nr_replicates \\
+            --run_name $analysis_id \\
+            --matrix $matrix \\
+            --highest_mz_file $highest_mz_file \\
+            --breaks_filepath $breaks_file
         """
 }
 
diff --git a/DIMS/CollectFilled.R b/DIMS/CollectFilled.R
index 4bd408e..265db5d 100755
--- a/DIMS/CollectFilled.R
+++ b/DIMS/CollectFilled.R
@@ -1,14 +1,17 @@
-## adapted from 10-collectSamplesFilled.R
+# load package
+library("argparse")
 
-# define parameters
-cmd_args <- commandArgs(trailingOnly = TRUE)
+parser <- ArgumentParser(description = "CollectFilled")
 
-scripts_dir <- cmd_args[1]
-ppm <- as.numeric(cmd_args[2])
-z_score <- as.numeric(cmd_args[3])
+parser$add_argument("--scripts_dir", dest = "scripts_dir",
+                    help = "File path to the directory containing functions used in this script", required = TRUE)
+parser$add_argument("-z", "--z_score", dest = "z_score", type = "integer",
+                    help = "Numeric value, z-score = 1", required = TRUE)
 
-source(paste0(scripts_dir, "merge_duplicate_rows.R"))
-source(paste0(scripts_dir, "calculate_zscores.R"))
+args <- parser$parse_args()
+
+source(paste0(args$scripts_dir, "merge_duplicate_rows.R"))
+source(paste0(args$scripts_dir, "calculate_zscores.R"))
 
 # for each scan mode, collect all filled peak group lists
 scanmodes <- c("positive", "negative")
@@ -17,7 +20,7 @@ for (scanmode in scanmodes) {
   filled_files <- list.files("./", full.names = TRUE, pattern = paste0(scanmode, "_identified_filled"))
   # load files and combine into one object
   outlist_total <- NULL
-  for (file_nr in 1:length(filled_files)) {
+  for (file_nr in seq_along(filled_files)) {
     peakgrouplist_filled <- get(load(filled_files[file_nr]))
     outlist_total <- rbind(outlist_total, peakgrouplist_filled)
   }
@@ -29,7 +32,7 @@ for (scanmode in scanmodes) {
   pattern_file <- paste0(scanmode, "_repl_pattern.RData")
   repl_pattern <- get(load(pattern_file))
   # calculate Z-scores
-  if (z_score == 1) {
+  if (args$z_score == 1) {
     outlist_stats <- calculate_zscores(outlist_total, adducts = FALSE)
     nr_removed_samples <- length(which(repl_pattern[] == "character(0)"))
     order_index_int <- order(colnames(outlist_stats)[8:(length(repl_pattern) - nr_removed_samples + 7)])
@@ -47,7 +50,7 @@ for (scanmode in scanmodes) {
     outlist_stats_more <- cbind(outlist_stats_more, tmp)
     outlist_total <- outlist_stats_more
   }
-  
+
   # make a copy of the outlist
   outlist_ident <- outlist_total
   # take care of NAs in theormz_noise
diff --git a/DIMS/CollectFilled.nf b/DIMS/CollectFilled.nf
index 53b1967..1f17444 100644
--- a/DIMS/CollectFilled.nf
+++ b/DIMS/CollectFilled.nf
@@ -1,7 +1,7 @@
 process CollectFilled {
     tag "DIMS CollectFilled"
     label 'CollectFilled'
-    container = 'docker://umcugenbioinf/dims:1.3'
+    container = 'docker://umcugenbioinf/dims:1.4'
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
@@ -14,6 +14,8 @@ process CollectFilled {
 
     script:
         """
-        Rscript ${baseDir}/CustomModules/DIMS/CollectFilled.R $params.scripts_dir $params.ppm $params.zscore
+        Rscript ${baseDir}/CustomModules/DIMS/CollectFilled.R \\
+            --scripts_dir $params.scripts_dir \\
+            --z_score $params.zscore
         """
 }
diff --git a/DIMS/CollectSumAdducts.R b/DIMS/CollectSumAdducts.R
index 28b5bf0..10752ad 100755
--- a/DIMS/CollectSumAdducts.R
+++ b/DIMS/CollectSumAdducts.R
@@ -1,13 +1,16 @@
 ## Combining all AdductSums part files for each scanmode and
 # combine intensities if present in both scanmodes
+library("argparse")
 suppressMessages(library("dplyr"))
 
-# define parameters
-cmd_args <- commandArgs(trailingOnly = TRUE)
+parser <- ArgumentParser(description = "GenerateExcel")
 
-preprocessing_scripts_dir <- cmd_args[1]
+parser$add_argument("--preprocessing_scripts_dir", dest = "preprocessing_scripts_dir",
+                    help = "File path to the directory containing functions used in this script", required = TRUE)
 
-source(paste0(preprocessing_scripts_dir, "collect_sum_adducts_functions.R"))
+args <- parser$parse_args()
+
+source(paste0(args$preprocessing_scripts_dir, "collect_sum_adducts_functions.R"))
 
 # collect all AdductSums part files for each scanmode and save to RData file
 outlist_tot_pos <- combine_sum_adduct_parts("positive")
diff --git a/DIMS/CollectSumAdducts.nf b/DIMS/CollectSumAdducts.nf
index 279cd0e..06aa82c 100644
--- a/DIMS/CollectSumAdducts.nf
+++ b/DIMS/CollectSumAdducts.nf
@@ -1,7 +1,7 @@
 process CollectSumAdducts {
     tag "DIMS CollectSumAdducts"
     label 'CollectSumAdducts'
-    container = 'docker://umcugenbioinf/dims:1.3'
+    container = 'docker://umcugenbioinf/dims:1.4'
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
@@ -13,6 +13,7 @@ process CollectSumAdducts {
 
     script:
         """
-        Rscript ${baseDir}/CustomModules/DIMS/CollectSumAdducts.R $params.preprocessing_scripts_dir
+        Rscript ${baseDir}/CustomModules/DIMS/CollectSumAdducts.R \\
+        --preprocessing_scripts_dir $params.preprocessing_scripts_dir
         """
 }
diff --git a/DIMS/FillMissing.nf b/DIMS/FillMissing.nf
index b0d1850..7678c95 100644
--- a/DIMS/FillMissing.nf
+++ b/DIMS/FillMissing.nf
@@ -1,7 +1,7 @@
 process FillMissing {
     tag "DIMS FillMissing ${peakgrouplist_file}"
     label 'FillMissing'
-    container = 'docker://umcugenbioinf/dims:1.3'
+    container = 'docker://umcugenbioinf/dims:1.4'
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
diff --git a/DIMS/GenerateBreaks.R b/DIMS/GenerateBreaks.R
index d07fd20..0943c32 100644
--- a/DIMS/GenerateBreaks.R
+++ b/DIMS/GenerateBreaks.R
@@ -1,15 +1,17 @@
-## adapted from 1-generateBreaksFwhm.HPC.R ##
-
-# load required package
+# load required packages
+load("argparse")
 suppressPackageStartupMessages(library("xcms"))
 
-# define parameters
-cmd_args <- commandArgs(trailingOnly = TRUE)
+parser <- ArgumentParser(description = "GenerateBreaks")
+
+parser$add_argument("--raw_file", dest = "raw_filepath",
+                    help = "File path to a raw file", required = TRUE)
+parser$add_argument("--trim", dest = "trim", type = "integer",
+                    help = "Trim precentage, numeric value", required = TRUE)
+parser$add_argument("--resolution", dest = "resolution", type = "integer",
+                    help = "Resolution of the MS machine, numeric value", required = TRUE)
 
-filepath <- cmd_args[1]
-outdir <- cmd_args[2]
-trim <- as.numeric(cmd_args[3])
-resol <- as.numeric(cmd_args[4])
+args <- parser$parse_args()
 
 # initialize
 trim_left_pos <- NULL
@@ -21,19 +23,19 @@ breaks_fwhm_avg <- NULL
 bins <- NULL
 
 # read in mzML file
-raw_data <- suppressMessages(xcms::xcmsRaw(filepath))
+raw_data <- suppressMessages(xcms::xcmsRaw(args$raw_filepath))
 
 # 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
+trim_left_pos  <- round(pos_times[length(pos_times) * (args$trim * 1.5)]) # 15% aan het begin
+trim_right_pos <- round(pos_times[length(pos_times) * (1 - (args$trim * 0.5))]) # 5% aan het eind
 
 # 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)])
+trim_left_neg  <- round(neg_times[length(neg_times) * args$trim])
+trim_right_neg <- round(neg_times[length(neg_times) * (1 - args$trim)])
 
 # Mass range m/z
 low_mz  <- raw_data@mzrange[1]
@@ -46,8 +48,8 @@ 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)))
+  end_segment <- segment[i + 1]
+  resol_mz <- args$resolution * (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
diff --git a/DIMS/GenerateBreaks.nf b/DIMS/GenerateBreaks.nf
index af617a8..ac0c284 100644
--- a/DIMS/GenerateBreaks.nf
+++ b/DIMS/GenerateBreaks.nf
@@ -1,7 +1,7 @@
 process GenerateBreaks {
     tag "DIMS GenerateBreaks"
     label 'GenerateBreaks'
-    container = 'docker://umcugenbioinf/dims:1.3'
+    container = 'docker://umcugenbioinf/dims:1.4'
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
@@ -14,6 +14,9 @@ process GenerateBreaks {
 
     script:
         """
-        Rscript ${baseDir}/CustomModules/DIMS/GenerateBreaks.R $mzML_file ./ $params.trim $params.resolution 
+        Rscript ${baseDir}/CustomModules/DIMS/GenerateBreaks.R \\
+            --raw_file $mzML_file \\
+            --trim $params.trim \\
+            --resolution $params.resolution 
         """
 }
diff --git a/DIMS/GenerateExcel.R b/DIMS/GenerateExcel.R
index 5366264..fda09e7 100644
--- a/DIMS/GenerateExcel.R
+++ b/DIMS/GenerateExcel.R
@@ -1,4 +1,5 @@
 # load required packages
+library("argparse")
 library("ggplot2")
 library("reshape2")
 library("openxlsx")
@@ -6,17 +7,23 @@ suppressMessages(library("tidyr"))
 suppressMessages(library("dplyr"))
 suppressMessages(library("stringr"))
 
-# define parameters
-cmd_args <- commandArgs(trailingOnly = TRUE)
+parser <- ArgumentParser(description = "GenerateExcel")
 
-project <- cmd_args[1]
-hmdb_rlvc_file <- cmd_args[2]
-z_score <- as.numeric(cmd_args[3])
-export_scripts_dir <- cmd_args[4]
-path_metabolite_groups <- cmd_args[5]
+parser$add_argument("--project", dest = "project",
+                    help = "Project name", required = TRUE)
+parser$add_argument("--hmdb_rlvc_file", dest = "hmdb_rlvc_file",
+                    help = "File path to the HMDB relevance file", required = TRUE)
+parser$add_argument("-z", "--z_score", dest = "z_score", type = "integer",
+                    help = "Numeric value, z-score = 1", required = TRUE)
+parser$add_argument("--export_scripts_dir", dest = "export_scripts_dir",
+                    help = "File path to the directory containing functions used in this script", required = TRUE)
+parser$add_argument("--path_metabolite_groups", dest = "path_metabolite_groups",
+                    help = "File path to the directory containing the metabolite groups", required = TRUE)
+
+args <- parser$parse_args()
 
 # load in function scripts
-source(paste0(export_scripts_dir, "generate_excel_functions.R"))
+source(paste0(args$export_scripts_dir, "generate_excel_functions.R"))
 
 # set the number of digits for floats
 options(digits = 16)
@@ -35,7 +42,7 @@ perc <- 5
 outlier_threshold <- 2
 
 # load HMDB rlvnc table
-load(hmdb_rlvc_file)
+load(args$hmdb_rlvc_file)
 
 # load outlist object
 load("AdductSums_combined.RData")
@@ -64,7 +71,7 @@ wb_intensities <- openxlsx::createWorkbook("SinglePatient")
 openxlsx::addWorksheet(wb_intensities, sheetname)
 
 # Add Z-scores and create plots
-if (z_score == 1) {
+if (args$z_score == 1) {
   dir.create(paste0(outdir, "/plots"), showWarnings = FALSE)
   wb_helix_intensities <- openxlsx::createWorkbook("SinglePatient")
   openxlsx::addWorksheet(wb_helix_intensities, sheetname)
@@ -121,13 +128,13 @@ if (z_score == 1) {
 
   # get Helix IDs for extra Excel file
   metabolite_files <- list.files(
-    path = paste(path_metabolite_groups, "Diagnostics", sep = "/"),
+    path = paste(args$path_metabolite_groups, "Diagnostics", sep = "/"),
     pattern = "*.txt", full.names = FALSE, recursive = FALSE
   )
   metab_df_helix <- NULL
   for (file_index in seq_along(metabolite_files)) {
     infile <- metabolite_files[file_index]
-    metab_list <- read.table(paste(path_metabolite_groups, "Diagnostics", infile, sep = "/"),
+    metab_list <- read.table(paste(args$path_metabolite_groups, "Diagnostics", infile, sep = "/"),
       sep = "\t", header = TRUE, quote = ""
     )
     metab_df_helix <- rbind(metab_df_helix, metab_list)
@@ -243,7 +250,7 @@ if (z_score == 1) {
     plots_present = TRUE
   )
   openxlsx::writeData(wb_helix_intensities, sheet = 1, outlist_helix, startCol = 1)
-  openxlsx::saveWorkbook(wb_helix_intensities, paste0(outdir, "/Helix_", project, ".xlsx"), overwrite = TRUE)
+  openxlsx::saveWorkbook(wb_helix_intensities, paste0(outdir, "/Helix_", args$project, ".xlsx"), overwrite = TRUE)
   rm(wb_helix_intensities)
 
   # reorder outlist for Excel file
@@ -267,6 +274,6 @@ if (z_score == 1) {
 
 # write Excel file
 openxlsx::writeData(wb_intensities, sheet = 1, outlist, startCol = 1)
-openxlsx::saveWorkbook(wb_intensities, paste0(outdir, "/", project, ".xlsx"), overwrite = TRUE)
+openxlsx::saveWorkbook(wb_intensities, paste0(outdir, "/", args$project, ".xlsx"), overwrite = TRUE)
 rm(wb_intensities)
 unlink("plots", recursive = TRUE)
diff --git a/DIMS/GenerateExcel.nf b/DIMS/GenerateExcel.nf
index 552a8ee..21fefd4 100644
--- a/DIMS/GenerateExcel.nf
+++ b/DIMS/GenerateExcel.nf
@@ -1,7 +1,7 @@
 process GenerateExcel {
     tag "DIMS GenerateExcel"
     label 'GenerateExcel'
-    container = 'docker://umcugenbioinf/dims:1.3'
+    container = 'docker://umcugenbioinf/dims:1.4'
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
@@ -18,6 +18,11 @@ process GenerateExcel {
 
     script:
         """
-        Rscript ${baseDir}/CustomModules/DIMS/GenerateExcel.R $analysis_id $relevance_file $params.zscore $params.export_scripts_dir $params.path_metabolite_groups
+        Rscript ${baseDir}/CustomModules/DIMS/GenerateExcel.R \\
+            --project $analysis_id \\
+            --hmdb_rlvc_file $relevance_file \\
+            --z_score $params.zscore \\
+            --export_scripts_dir $params.export_scripts_dir \\
+            --path_metabolite_groups $params.path_metabolite_groups
         """
 }
diff --git a/DIMS/GenerateQCOutput.R b/DIMS/GenerateQCOutput.R
index 4e3394d..2bc87a5 100644
--- a/DIMS/GenerateQCOutput.R
+++ b/DIMS/GenerateQCOutput.R
@@ -1,3 +1,4 @@
+library("argparse")
 library("ggplot2")
 library("reshape2")
 library("openxlsx")
@@ -6,23 +7,30 @@ suppressMessages(library("dplyr"))
 # set the number of digits for floats
 options(digits = 16)
 
-# define parameters
-cmd_args <- commandArgs(trailingOnly = TRUE)
+parser <- ArgumentParser(description = "GenerateQCOutput")
 
-init_file <- cmd_args[1]
-project <- cmd_args[2]
-dims_matrix <- cmd_args[3]
-z_score <- cmd_args[4]
-sst_components_file <- cmd_args[5]
-export_scripts_dir <- cmd_args[6]
+parser$add_argument("--init_file_path", dest = "init_file",
+                    help = "File path for the init RData file", required = TRUE)
+parser$add_argument("--project", dest = "project",
+                    help = "Project name", required = TRUE)
+parser$add_argument("--matrix", dest = "dims_matrix",
+                    help = "The matrix used, e.g. Plasma, Research, ...", required = TRUE)
+parser$add_argument("-z", "--z_score", dest = "z_score", type = "integer",
+                    help = "Numeric value, z-score = 1", required = TRUE)
+parser$add_argument("--sst_components_file", dest = "sst_components_file",
+                    help = "File path to the SST components file", required = TRUE)
+parser$add_argument("--export_scripts_dir", dest = "export_scripts_dir",
+                    help = "File path to the directory containing functions used in this script", required = TRUE)
+
+args <- parser$parse_args()
 
 outdir <- "./"
 
 # load in function scripts
-source(paste0(export_scripts_dir, "generate_qc_output_functions.R"))
+source(paste0(args$export_scripts_dir, "generate_qc_output_functions.R"))
 
 # load init files
-load(init_file)
+load(args$init_file)
 # load outlist from GenerateExcel
 load("outlist.RData")
 # load combined adducts for each scanmodus
@@ -38,7 +46,7 @@ dir.create(paste0(outdir, "/plots"), showWarnings = FALSE)
 control_label <- "C"
 
 #### CHECK NUMBER OF CONTROLS ####
-if (z_score == 1) {
+if (args$z_score == 1) {
   file_name <- "Check_number_of_controls.txt"
   min_num_controls <- 25
   check_number_of_controls(outlist, min_num_controls, file_name)
@@ -67,14 +75,14 @@ outlist_tot_neg <- outlist_tot_neg[, samples_both_modes]
 outlist_tot_pos <- outlist_tot_pos[, samples_both_modes]
 
 # Retrieve IS summed adducts
-is_summed <- get_internal_standards(is_list, "summed", repl_pattern, dims_matrix, rundate, project)
+is_summed <- get_internal_standards(is_list, "summed", repl_pattern, args$dims_matrix, rundate, args$project)
 # Retrieve IS positive mode
-is_pos <- get_internal_standards(is_list, "pos", outlist_tot_pos, dims_matrix, rundate, project)
+is_pos <- get_internal_standards(is_list, "pos", outlist_tot_pos, args$dims_matrix, rundate, args$project)
 # Retrieve IS negative mode
-is_neg <- get_internal_standards(is_list, "neg", outlist_tot_neg, dims_matrix, rundate, project)
+is_neg <- get_internal_standards(is_list, "neg", outlist_tot_neg, args$dims_matrix, rundate, args$project)
 
 # Save results
-save(is_pos, is_neg, is_summed, file = paste0(outdir, "/", project, "_IS_results.RData"))
+save(is_pos, is_neg, is_summed, file = paste0(outdir, "/", args$project, "_IS_results.RData"))
 
 # number of samples, for plotting length and width
 sample_count <- length(repl_pattern)
@@ -138,7 +146,7 @@ is_sum_selection <- c(
 )
 
 # add minimal intensity lines based on matrix (DBS or Plasma) and machine mode (neg, pos, sum)
-if (dims_matrix == "DBS") {
+if (args$dims_matrix == "DBS") {
   add_min_intens_lines <- TRUE
   hline_data_neg <-
     data.frame(
@@ -155,7 +163,7 @@ if (dims_matrix == "DBS") {
       int_line = c(1300000, 2500000, 500000, 1800000, 1400000),
       HMDB_name = is_sum_selection
     )
-} else if (dims_matrix == "Plasma") {
+} else if (args$dims_matrix == "Plasma") {
   add_min_intens_lines <- TRUE
   hline_data_neg <-
     data.frame(
@@ -239,7 +247,7 @@ patterns <- c("^(P1002\\.)[[:digit:]]+_", "^(P1003\\.)[[:digit:]]+_", "^(P1005\\
 positive_controls_index <- grepl(pattern = paste(patterns, collapse = "|"), column_list)
 positive_control_list <- column_list[positive_controls_index]
 
-if (z_score == 1) {
+if (args$z_score == 1) {
   # find if one or more positive control samples are missing
   pos_contr_warning <- c()
   if (all(sapply(c("^P1002", "^P1003", "^P1005"),
@@ -280,16 +288,16 @@ if (z_score == 1) {
 
     positive_control$Zscore <- as.numeric(positive_control$Zscore)
     # extra information added to excel for future reference. made in beginning of this script
-    positive_control$Matrix <- dims_matrix
+    positive_control$Matrix <- args$dims_matrix
     positive_control$Rundate <- rundate
-    positive_control$Project <- project
+    positive_control$Project <- args$project
 
     # Save results
-    save(positive_control, file = paste0(outdir, "/", project, "_positive_control.RData"))
+    save(positive_control, file = paste0(outdir, "/", args$project, "_positive_control.RData"))
     # round the Z-scores to 2 digits
     positive_control$Zscore <- round_df(positive_control$Zscore, 2)
     write.xlsx(positive_control,
-      file = paste0(outdir, "/", project, "_positive_control.xlsx"),
+      file = paste0(outdir, "/", args$project, "_positive_control.xlsx"),
       sheetName = "Sheet1", col.names = TRUE, row.names = TRUE, append = FALSE
     )
   }
@@ -315,7 +323,7 @@ is_neg_intensities <- get_is_intensities(outlist_tot_neg, is_codes = is_codes)
 is_pos_intensities <- get_is_intensities(outlist_tot_pos, is_codes = is_codes)
 
 # SST components.
-sst_comp <- read.csv(sst_components_file, header = TRUE, sep = "\t")
+sst_comp <- read.csv(args$sst_components_file, header = TRUE, sep = "\t")
 sst_list <- outlist %>% filter(HMDB_code %in% sst_comp$HMDB_ID)
 sst_colnrs <- grep("P1001", colnames(sst_list))
 
@@ -352,7 +360,7 @@ setColWidths(wb, 3, cols = 1, widths = 24)
 addWorksheet(wb, "SST components")
 openxlsx::writeData(wb, sheet = 4, sst_list_intensities)
 setColWidths(wb, 4, cols = 1:3, widths = 24)
-xlsx_name <- paste0(outdir, "/", project, "_IS_SST.xlsx")
+xlsx_name <- paste0(outdir, "/", args$project, "_IS_SST.xlsx")
 openxlsx::saveWorkbook(wb, xlsx_name, overwrite = TRUE)
 rm(wb)
 
diff --git a/DIMS/GenerateQCOutput.nf b/DIMS/GenerateQCOutput.nf
index eb17301..6e4c994 100644
--- a/DIMS/GenerateQCOutput.nf
+++ b/DIMS/GenerateQCOutput.nf
@@ -1,7 +1,7 @@
 process GenerateQCOutput {
     tag "DIMS GenerateQCOutput"
     label 'GenerateQCOutput'
-    container = 'docker://umcugenbioinf/dims:1.3'
+    container = 'docker://umcugenbioinf/dims:1.4'
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
@@ -20,11 +20,12 @@ process GenerateQCOutput {
 
     script:
         """
-        Rscript ${baseDir}/CustomModules/DIMS/GenerateQCOutput.R $init_file \
-                                                                 $analysis_id \
-                                                                 $params.matrix \
-                                                                 $params.zscore \
-                                                                 $params.sst_components_file \
-                                                                 $params.export_scripts_dir
+        Rscript ${baseDir}/CustomModules/DIMS/GenerateQCOutput.R \\
+            --init_file_path $init_file \\
+            --project $analysis_id \\
+            --matrix $params.matrix \\
+            --z_score $params.zscore \\
+            --sst_components_file $params.sst_components_file \\
+            --export_scripts_dir $params.export_scripts_dir
         """
 }
diff --git a/DIMS/GenerateViolinPlots.nf b/DIMS/GenerateViolinPlots.nf
index 1c4b532..6136ec3 100755
--- a/DIMS/GenerateViolinPlots.nf
+++ b/DIMS/GenerateViolinPlots.nf
@@ -1,7 +1,7 @@
 process GenerateViolinPlots {
     tag "DIMS GenerateViolinPlots"
     label 'GenerateViolinPlots'
-    container = 'docker://umcugenbioinf/dims:1.3'
+    container = 'docker://umcugenbioinf/dims:1.4'
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
diff --git a/DIMS/HMDBparts.nf b/DIMS/HMDBparts.nf
index 5f19f75..4b1fa5a 100644
--- a/DIMS/HMDBparts.nf
+++ b/DIMS/HMDBparts.nf
@@ -1,7 +1,7 @@
 process HMDBparts {
     tag "DIMS HMDBparts"
     label 'HMDBparts'
-    container = 'docker://umcugenbioinf/dims:1.3'
+    container = 'docker://umcugenbioinf/dims:1.4'
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
diff --git a/DIMS/HMDBparts_main.R b/DIMS/HMDBparts_main.R
index 14335bf..c1bb218 100644
--- a/DIMS/HMDBparts_main.R
+++ b/DIMS/HMDBparts_main.R
@@ -1,34 +1,38 @@
-## adapted from hmdb_part_adductSums.R
+# load package
+load("argparse")
 
-# define parameters 
-cmd_args <- commandArgs(trailingOnly = TRUE)
+parser <- ArgumentParser(description = "HMDBparts_main")
 
-db_file <- cmd_args[1]
-breaks_file <- cmd_args[2]
+parser$add_argument("--hmdb_db_file", dest = "hmdb_db_file",
+                    help = "File path the HMDB databse file", required = TRUE)
+parser$add_argument("--breaks_file", dest = "breaks_file",
+                    help = "File containing all the breaks/bins", required = TRUE)
 
-load(db_file)
-load(breaks_file)
+args <- parser$parse_args()
 
-# Cut up HMDB minus adducts minus isotopes into small parts 
+load(args$db_file)
+load(args$breaks_file)
+
+# Cut up HMDB minus adducts minus isotopes into small parts
 scanmodes <- c("positive", "negative")
 for (scanmode in scanmodes) {
   if (scanmode == "negative") {
     column_label <- "MNeg"
-    HMDB_add_iso <- HMDB_add_iso.Neg
+    hmdb_add_iso <- HMDB_add_iso.Neg
   } else if (scanmode == "positive") {
     column_label <- "Mpos"
-    HMDB_add_iso <- HMDB_add_iso.Pos
+    hmdb_add_iso <- HMDB_add_iso.Pos
   }
 
   # filter mass range measured
-  outlist <- HMDB_add_iso[which(HMDB_add_iso[ , column_label] >= breaks_fwhm[1] & 
-             HMDB_add_iso[ ,column_label] <= breaks_fwhm[length(breaks_fwhm)]), ]
+  outlist <- hmdb_add_iso[which(hmdb_add_iso[, column_label] >= breaks_fwhm[1] &
+                                  hmdb_add_iso[, column_label] <= breaks_fwhm[length(breaks_fwhm)]), ]
 
   # remove adducts and isotopes, put internal standard at the beginning
   outlist <- outlist[grep("HMDB", rownames(outlist), fixed = TRUE), ]
   outlist <- outlist[-grep("_", rownames(outlist), fixed = TRUE), ]
   # sort on m/z value
-  outlist <- outlist[order(outlist[ , column_label]), ]
+  outlist <- outlist[order(outlist[, column_label]), ]
   nr_rows <- dim(outlist)[1]
 
   # size of hmdb parts in lines:
@@ -37,12 +41,12 @@ for (scanmode in scanmodes) {
   check <- 0
 
   # generate hmdb parts
-  if (nr_rows >= sub & (floor(nr_rows / sub)) >= 2) {
+  if (nr_rows >= sub && (floor(nr_rows / sub)) >= 2) {
     for (i in 1:floor(nr_rows / sub)) {
       start <- -(sub - 1) + i * sub
       end <- i * sub
       outlist_part <- outlist[c(start:end), ]
-      save(outlist_part, file=paste0(scanmode, "_hmdb_main.", i, ".RData"))
+      save(outlist_part, file = paste0(scanmode, "_hmdb_main.", i, ".RData"))
     }
   }
 
@@ -53,4 +57,4 @@ for (scanmode in scanmodes) {
   outlist_part <- outlist[c(start:end), ]
   save(outlist_part, file = paste0(scanmode, "_hmdb_main.", i + 1, ".RData"))
 
-}
\ No newline at end of file
+}
diff --git a/DIMS/HMDBparts_main.nf b/DIMS/HMDBparts_main.nf
index b38bac0..2ae3457 100644
--- a/DIMS/HMDBparts_main.nf
+++ b/DIMS/HMDBparts_main.nf
@@ -1,7 +1,7 @@
 process HMDBparts_main {
     tag "DIMS HMDBparts_main"
     label 'HMDBparts_main'
-    container = 'docker://umcugenbioinf/dims:1.3'
+    container = 'docker://umcugenbioinf/dims:1.4'
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
@@ -14,6 +14,8 @@ process HMDBparts_main {
     script:
 
         """
-        Rscript ${baseDir}/CustomModules/DIMS/HMDBparts_main.R $hmdb_db_file $breaks_file 
+        Rscript ${baseDir}/CustomModules/DIMS/HMDBparts_main.R \\
+            --hmdb_db_file $hmdb_db_file \\
+            --breaks_file $breaks_file 
         """
 }
diff --git a/DIMS/MakeInit.R b/DIMS/MakeInit.R
index 44d4996..d5f0570 100644
--- a/DIMS/MakeInit.R
+++ b/DIMS/MakeInit.R
@@ -1,14 +1,18 @@
-## adapted from makeInit in old pipeline
+# load required packages
+library("argparse")
 
-# define parameters
-args <- commandArgs(trailingOnly = TRUE)
+parser <- ArgumentParser(description = "MakeInit")
 
-sample_sheet <- read.csv(args[1], sep = "\t")
-nr_replicates <- as.numeric(args[2])
+parser$add_argument("--sample_sheet", dest = "sample_sheet",
+                    help = "Samplesheet txt file", required = TRUE)
+parser$add_argument("--nr_replicates", dest = "nr_replicates", type = "integer",
+                    help = "Number of replicates, numeric value", required = TRUE)
 
-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])))
+args <- parser$parse_args()
+
+sample_names <- trimws(as.vector(unlist(args$sample_sheet[1])))
+nr_sample_groups <- length(sample_names) / args$nr_replicates
+group_names <- trimws(as.vector(unlist(args$sample_sheet[2])))
 group_names <- gsub("[^-.[:alnum:]]", "_", group_names)
 group_names_unique <- unique(group_names)
 
@@ -16,8 +20,8 @@ group_names_unique <- unique(group_names)
 repl_pattern <- c()
 for (sample_group in 1:nr_sample_groups) {
   tmp <- c()
-  for (repl in nr_replicates:1) {
-    index <- ((sample_group * nr_replicates) - repl) + 1
+  for (repl in args$nr_replicates:1) {
+    index <- ((sample_group * args$nr_replicates) - repl) + 1
     tmp <- c(tmp, sample_names[index])
   }
   repl_pattern <- c(repl_pattern, list(tmp))
diff --git a/DIMS/MakeInit.nf b/DIMS/MakeInit.nf
index 7aae0e4..793d8f0 100644
--- a/DIMS/MakeInit.nf
+++ b/DIMS/MakeInit.nf
@@ -1,7 +1,7 @@
 process MakeInit {
     tag "DIMS MakeInit"
     label 'MakeInit'
-    container = 'docker://umcugenbioinf/dims:1.3'
+    container = 'docker://umcugenbioinf/dims:1.4'
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
@@ -13,6 +13,8 @@ process MakeInit {
 
     script:
         """
-        Rscript ${baseDir}/CustomModules/DIMS/MakeInit.R $samplesheet $nr_replicates 
+        Rscript ${baseDir}/CustomModules/DIMS/MakeInit.R \\
+            --samplesheet $samplesheet \\
+            --nr_replicates $nr_replicates 
         """
 }
diff --git a/DIMS/PeakFinding.nf b/DIMS/PeakFinding.nf
index 0097d12..0e25893 100644
--- a/DIMS/PeakFinding.nf
+++ b/DIMS/PeakFinding.nf
@@ -1,7 +1,7 @@
 process PeakFinding {
     tag "DIMS PeakFinding ${rdata_file}"
     label 'PeakFinding'
-    container = 'docker://umcugenbioinf/dims:1.3'
+    container = 'docker://umcugenbioinf/dims:1.4'
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
diff --git a/DIMS/PeakGrouping.nf b/DIMS/PeakGrouping.nf
index 0ecb18c..7f3f17e 100644
--- a/DIMS/PeakGrouping.nf
+++ b/DIMS/PeakGrouping.nf
@@ -1,7 +1,7 @@
 process PeakGrouping {
     tag "DIMS PeakGrouping ${hmdbpart_file}"
     label 'PeakGrouping'
-    container = 'docker://umcugenbioinf/dims:1.3'
+    container = 'docker://umcugenbioinf/dims:1.4'
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
diff --git a/DIMS/SpectrumPeakFinding.nf b/DIMS/SpectrumPeakFinding.nf
index 3590265..a8ae5a8 100644
--- a/DIMS/SpectrumPeakFinding.nf
+++ b/DIMS/SpectrumPeakFinding.nf
@@ -1,7 +1,7 @@
 process SpectrumPeakFinding {
     tag "DIMS SpectrumPeakFinding"
     label 'SpectrumPeakFinding'
-    container = 'docker://umcugenbioinf/dims:1.3'
+    container = 'docker://umcugenbioinf/dims:1.4'
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
diff --git a/DIMS/SumAdducts.nf b/DIMS/SumAdducts.nf
index 4b3f965..a667e6e 100644
--- a/DIMS/SumAdducts.nf
+++ b/DIMS/SumAdducts.nf
@@ -1,7 +1,7 @@
 process SumAdducts {
     tag "DIMS SumAdducts ${hmdbpart_main_file}"
     label 'SumAdducts'
-    container = 'docker://umcugenbioinf/dims:1.3'
+    container = 'docker://umcugenbioinf/dims:1.4'
     shell = ['/bin/bash', '-euo', 'pipefail']
 
     input: