diff --git a/docs/output.md b/docs/output.md
index 8974a1e..9251e4e 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -73,6 +73,7 @@ The directories listed below will be created in the results directory after the
 │   ├── sample.normal_alleleFrequencies_chr(1-22,X).txt
 │   ├── sample.purityploidy.txt
 │   ├── sample.segments.txt
+│   ├── sample.segments_raw.txt
 │   ├── sample.tumour_alleleFrequencies_chr(1-22,X).txt
 │   ├── sample.tumour_normalBAF_rawBAF.txt
 │   ├── sample.tumour_normalBAF.txt
@@ -92,6 +93,7 @@ The directories listed below will be created in the results directory after the
 | `sample.normal_alleleFrequencies_chr(1-22,X).txt`     | a tsv file describing the snp counts for the normal sample at each position and their respective depths          |
 | `sample.purityploidy.txt`                             | a tsv file describing the purity and ploidy values of the sample                                                 |
 | `sample.segments.txt`                                 | a tsv file describing each chromosome segment and it's major and minor copy number                               |
+| `sample.segments_raw.txt`                             | a tsv file describing each chromosome segment and it's major and minor rounded and raw copy number               |
 | `sample.tumour_alleleFrequencies_chr(1-22,X).txt`     | a tsv file describing the snp counts for the tumor sample at each position and their respective depths           |
 | `sample.tumour_normalBAF_rawBAF.txt`                  | a tsv file with the raw BAF values in the normal sample                                                          |
 | `sample.tumour_normalBAF.txt`                         | a tsv file with the BAF values in the normal sample                                                              |
diff --git a/docs/usage.md b/docs/usage.md
index dc14d04..448cf7d 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -153,6 +153,7 @@ You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-c
 | `--ascat_loci_files`          | A full path to a zipped folder containing loci files for [ASCAT](https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS). Must be zipped and have `.zip` format. Default = `null`                               |
 | `--ascat_gc_file`             | A full path to a GC correction file for [ASCAT](https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS). Optionally can be zipped and have either `.txt` or `.txt.zip` format. Default = `null`                 |
 | `--ascat_rt_file`             | A full path to a replication timing correction file for [ASCAT](https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS). Optionally can be zipped and have either `.txt` or `.txt.zip` format. Default = `null` |
+| `--ascat_pdf_plots`           | string to enable output pltos in pdf format. Default = `false`                                                                                                                                                              |
 
 ### Updating the pipeline
 
diff --git a/modules/nf-core/ascat/ascat.diff b/modules/nf-core/ascat/ascat.diff
index 7f93901..a022286 100644
--- a/modules/nf-core/ascat/ascat.diff
+++ b/modules/nf-core/ascat/ascat.diff
@@ -1,6 +1,4 @@
-Changes in component 'nf-core/ascat'
-'modules/nf-core/ascat/meta.yml' is unchanged
-Changes in 'ascat/main.nf':
+Changes in module 'nf-core/ascat'
 --- modules/nf-core/ascat/main.nf
 +++ modules/nf-core/ascat/main.nf
 @@ -1,211 +1,189 @@
@@ -98,7 +96,7 @@ Changes in 'ascat/main.nf':
 +    def penalty        = args.penalty         ?  "$args.penalty" :       "NULL"
 +    def gc_input       = gc_file              ?  "$gc_file" :            "NULL"
 +    def rt_input       = rt_file              ?  "$rt_file" :            "NULL"
-+
++    def pdf_plots      = (args.pdf_plots ?: false) ? "TRUE" : "FALSE"
 +    def minCounts_arg                    = args.minCounts                     ?  ",minCounts = $args.minCounts" : ""
 +    def bed_file_arg                     = bed_file                           ?  ",BED_file = '$bed_file'": ""
 +    def chrom_names_arg                  = args.chrom_names                   ?  ",chrom_names = $args.chrom_names" : ""
@@ -112,7 +110,7 @@ Changes in 'ascat/main.nf':
 +    def normal_bam                       = input_normal                       ? ",normalseqfile = '$input_normal'" : ""
 +    def normal_name                      = input_normal                       ? ",normalname = '${prefix}.normal'" : ""
 +    def longread_bins                    = args.longread_bins                 ? ",loci_binsize = $args.longread_bins" : ""
-+    def allele_counter_flags             = args.allele_counter_flags          ? ",additional_allelecounter_flags = '$args.allele_counter_flags'" : "" 
++    def allele_counter_flags             = args.allele_counter_flags          ? ",additional_allelecounter_flags = '$args.allele_counter_flags'" : ""
      """
      #!/usr/bin/env Rscript
      library(RColorBrewer)
@@ -318,16 +316,19 @@ Changes in 'ascat/main.nf':
 +    #Run ASCAT to fit every tumor to a model, inferring ploidy, normal cell contamination, and discrete copy numbers
 +    #If psi and rho are manually set:
 +    if (!is.null($purity) && !is.null($ploidy)){
-+        ascat.output <- ascat.runAscat(ascat.bc, gamma=1, rho_manual=$purity, psi_manual=$ploidy)
++        ascat.output <- ascat.runAscat(ascat.bc, gamma=1, rho_manual=$purity, psi_manual=$ploidy, pdfPlot = $pdf_plots)
 +    } else if(!is.null($purity) && is.null($ploidy)){
-+        ascat.output <- ascat.runAscat(ascat.bc, gamma=1, rho_manual=$purity)
++        ascat.output <- ascat.runAscat(ascat.bc, gamma=1, rho_manual=$purity, pdfPlot = $pdf_plots)
 +    } else if(!is.null($ploidy) && is.null($purity)){
-+        ascat.output <- ascat.runAscat(ascat.bc, gamma=1, psi_manual=$ploidy)
++        ascat.output <- ascat.runAscat(ascat.bc, gamma=1, psi_manual=$ploidy, pdfPlot = $pdf_plots)
      } else {
-         ascat.output <- ascat.runAscat(ascat.bc, gamma=1)
-     }
- 
+-        ascat.output <- ascat.runAscat(ascat.bc, gamma=1)
+-    }
+-
 -    # Extract metrics from ASCAT profiles
++        ascat.output <- ascat.runAscat(ascat.bc, gamma=1, pdfPlot = $pdf_plots)
++    }
++
 +    #Extract metrics from ASCAT profiles
      QC = ascat.metrics(ascat.bc,ascat.output)
  
@@ -342,7 +343,7 @@ Changes in 'ascat/main.nf':
 +    tryCatch({ # In case segments_raw is not selected
 +      write.table(
 +        ascat.output[["segments_raw"]],
-+        file = paste0(prefix, ".segments_raw.txt"),
++        file = paste0("$prefix", ".segments_raw.txt"),
 +        sep = "\t", quote = FALSE, row.names = FALSE
 +      )
 +    }, error = function(e) {
@@ -360,7 +361,7 @@ Changes in 'ascat/main.nf':
      summary <- tryCatch({
              matrix(c(ascat.output[["aberrantcellfraction"]], ascat.output[["ploidy"]]), ncol=2, byrow=TRUE)}, error = function(err) {
                  # error handler picks up where error was generated
-@@ -214,46 +192,47 @@
+@@ -214,46 +192,48 @@
          }
      )
      colnames(summary) <- c("AberrantCellFraction","Ploidy")
@@ -426,6 +427,7 @@ Changes in 'ascat/main.nf':
 +    echo stub > ${prefix}.normal_alleleFrequencies_chr22.txt
 +    echo stub > ${prefix}.purityploidy.txt
 +    echo stub > ${prefix}.segments.txt
++    echo stub > ${prefix}.segments_raw.txt
 +    echo stub > ${prefix}.tumour.ASPCF.png
 +    echo stub > ${prefix}.tumour.sunrise.png
 +    echo stub > ${prefix}.tumour_alleleFrequencies_chr21.txt
@@ -437,13 +439,52 @@ Changes in 'ascat/main.nf':
 +
 +    echo "${task.process}:" > versions.yml
 +    echo ' alleleCounter: 4.3.0' >> versions.yml
-+    echo ' ascat: 3.0.0' >> versions.yml
++    echo ' ascat: 3.2.0' >> versions.yml
 +
 +    """
 +
 +}
-'modules/nf-core/ascat/environment.yml' is unchanged
-'modules/nf-core/ascat/tests/main.nf.test' is unchanged
-'modules/nf-core/ascat/tests/main.nf.test.snap' is unchanged
-'modules/nf-core/ascat/tests/nextflow.config' is unchanged
+--- modules/nf-core/ascat/tests/main.nf.test
++++ modules/nf-core/ascat/tests/main.nf.test
+@@ -55,6 +55,7 @@
+                     process.out.png.collect{it[1].collect{file(it).name}},
+                     process.out.purityploidy,
+                     process.out.segments,
++                    process.out.segments_raw,
+                     process.out.versions,
+                     path(process.out.versions[0]).yaml
+                 ).match() }
+@@ -109,6 +110,7 @@
+                     process.out.png.collect{it[1].collect{file(it).name}},
+                     process.out.purityploidy,
+                     process.out.segments,
++                    process.out.segments_raw,
+                     process.out.versions,
+                     path(process.out.versions[0]).yaml
+                 ).match() }
+@@ -163,6 +165,7 @@
+                     process.out.png.collect{it[1].collect{file(it).name}},
+                     process.out.purityploidy,
+                     process.out.segments,
++                    process.out.segments_raw,
+                     process.out.versions,
+                     path(process.out.versions[0]).yaml
+                 ).match() }
+@@ -218,6 +221,7 @@
+                     process.out.png.collect{it[1].collect{file(it).name}},
+                     process.out.purityploidy,
+                     process.out.segments,
++                    process.out.segments_raw,
+                     process.out.versions,
+                     path(process.out.versions[0]).yaml
+                 ).match() }
+@@ -296,6 +300,7 @@
+                     process.out.png.collect{it[1].collect{file(it).name}},
+                     process.out.purityploidy,
+                     process.out.segments,
++                    process.out.segments_raw,
+                     process.out.versions,
+                     path(process.out.versions[0]).yaml
+                 ).match() }
+
 ************************************************************
diff --git a/modules/nf-core/ascat/main.nf b/modules/nf-core/ascat/main.nf
index fb34f18..01641e1 100644
--- a/modules/nf-core/ascat/main.nf
+++ b/modules/nf-core/ascat/main.nf
@@ -42,8 +42,7 @@ process ASCAT {
     def penalty        = args.penalty         ?  "$args.penalty" :       "NULL"
     def gc_input       = gc_file              ?  "$gc_file" :            "NULL"
     def rt_input       = rt_file              ?  "$rt_file" :            "NULL"
-    def pdf_plots      = args.pdf_plots       ?  ("$args.pdf_plots" == true ? "TRUE": "FALSE") :     "NULL"
-
+    def pdf_plots      = (args.pdf_plots ?: false) ? "TRUE" : "FALSE"
     def minCounts_arg                    = args.minCounts                     ?  ",minCounts = $args.minCounts" : ""
     def bed_file_arg                     = bed_file                           ?  ",BED_file = '$bed_file'": ""
     def chrom_names_arg                  = args.chrom_names                   ?  ",chrom_names = $args.chrom_names" : ""
@@ -173,7 +172,7 @@ process ASCAT {
     tryCatch({ # In case segments_raw is not selected
       write.table(
         ascat.output[["segments_raw"]],
-        file = paste0(prefix, ".segments_raw.txt"),
+        file = paste0("$prefix", ".segments_raw.txt"),
         sep = "\t", quote = FALSE, row.names = FALSE
       )
     }, error = function(e) {
@@ -221,6 +220,7 @@ process ASCAT {
     echo stub > ${prefix}.normal_alleleFrequencies_chr22.txt
     echo stub > ${prefix}.purityploidy.txt
     echo stub > ${prefix}.segments.txt
+    echo stub > ${prefix}.segments_raw.txt
     echo stub > ${prefix}.tumour.ASPCF.png
     echo stub > ${prefix}.tumour.sunrise.png
     echo stub > ${prefix}.tumour_alleleFrequencies_chr21.txt
diff --git a/modules/nf-core/ascat/tests/main.nf.test b/modules/nf-core/ascat/tests/main.nf.test
index 527fbc2..759abb3 100644
--- a/modules/nf-core/ascat/tests/main.nf.test
+++ b/modules/nf-core/ascat/tests/main.nf.test
@@ -55,6 +55,7 @@ nextflow_process {
                     process.out.png.collect{it[1].collect{file(it).name}},
                     process.out.purityploidy,
                     process.out.segments,
+                    process.out.segments_raw,
                     process.out.versions,
                     path(process.out.versions[0]).yaml
                 ).match() }
@@ -109,6 +110,7 @@ nextflow_process {
                     process.out.png.collect{it[1].collect{file(it).name}},
                     process.out.purityploidy,
                     process.out.segments,
+                    process.out.segments_raw,
                     process.out.versions,
                     path(process.out.versions[0]).yaml
                 ).match() }
@@ -163,6 +165,7 @@ nextflow_process {
                     process.out.png.collect{it[1].collect{file(it).name}},
                     process.out.purityploidy,
                     process.out.segments,
+                    process.out.segments_raw,
                     process.out.versions,
                     path(process.out.versions[0]).yaml
                 ).match() }
@@ -218,6 +221,7 @@ nextflow_process {
                     process.out.png.collect{it[1].collect{file(it).name}},
                     process.out.purityploidy,
                     process.out.segments,
+                    process.out.segments_raw,
                     process.out.versions,
                     path(process.out.versions[0]).yaml
                 ).match() }
@@ -296,6 +300,7 @@ nextflow_process {
                     process.out.png.collect{it[1].collect{file(it).name}},
                     process.out.purityploidy,
                     process.out.segments,
+                    process.out.segments_raw,
                     process.out.versions,
                     path(process.out.versions[0]).yaml
                 ).match() }