ascat raw segments txt files added to output

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                                                              |

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