Update docs

docs/output.md

@@ -19,12 +19,13 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
         - [BWA-mem2](#bwa-mem2)
     - [Mark Duplicates](#mark-duplicates)
         - [GATK MarkDuplicates](#gatk-markduplicates)
+        - [GATK MarkDuplicates Spark](#gatk-markduplicates-spark)
     - [Base (Quality Score) Recalibration](#base-quality-score-recalibration)
-        - [GATK BaseRecalibrator](#gatk-baserecalibrator)
-        - [GATK ApplyBQSR](#gatk-applybqsr)
-    - [TSV files](#tsv-files)
-    - [TSV files with `--skip_markduplicates`](#tsv-files-with---skip_markduplicates)
-    - [TSV files with `--sentieon`](#tsv-files-with---sentieon)
+        - [GATK BaseRecalibrator (Spark)](#gatk-baserecalibrator)
+        - [GATK ApplyBQSR (Spark)](#gatk-applybqsr)
+    - [CSV files](#tsv-files)
+    - [CSV files with `--skip_markduplicates`](#csv-files-with---skip_markduplicates)
+    - [CSV files with `--sentieon`](#tsv-files-with---sentieon)
 - [Variant Calling](#variant-calling)
     - [SNVs and small indels](#snvs-and-small-indels)
         - [FreeBayes](#freebayes)
@@ -44,6 +45,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
         - [ConvertAlleleCounts](#convertallelecounts)
         - [ASCAT](#ascat)
         - [Control-FREEC](#control-freec)
+        - [CNVKit](#cnvkit)
     - [MSI status](#msi-status)
         - [MSIsensor](#msisensor)
 - [Variant annotation](#variant-annotation)
@@ -52,7 +54,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 - [QC and reporting](#qc-and-reporting)
     - [QC](#qc)
         - [FastQC](#fastqc)
-        - [bamQC](#bamqc)
+        - [Qualimap](#qualimap)
         - [GATK MarkDuplicates reports](#gatk-markduplicates-reports)
         - [samtools stats](#samtools-stats)
         - [bcftools stats](#bcftools-stats)
@@ -101,6 +103,8 @@ For all samples:
 
 For further reading and documentation see the [data pre-processing for variant discovery from the GATK best practices](https://gatk.broadinstitute.org/hc/en-us/articles/360035535912-Data-pre-processing-for-variant-discovery).
 
+#### GATK MarkDuplicates Spark
+
 ### Base (Quality Score) Recalibration
 
 #### GATK BaseRecalibrator
@@ -131,9 +135,9 @@ For all samples:
 
 For further reading and documentation see the [data pre-processing for variant discovery from the GATK best practices](https://gatk.broadinstitute.org/hc/en-us/articles/360035535912-Data-pre-processing-for-variant-discovery).
 
-### TSV files
+### CSV files
 
-The `TSV` files are auto-generated and can be used by `Sarek` for further processing and/or variant calling.
+The `CSV` files are auto-generated and can be used by `Sarek` for further processing and/or variant calling.
 
 For further reading and documentation see the [`--input`](usage.md#--input) section in the usage documentation.
 
@@ -146,7 +150,7 @@ For all samples:
 - `duplicates_marked_no_table_[SAMPLE].tsv`, `duplicates_marked_[SAMPLE].tsv` and `recalibrated_[SAMPLE].tsv`
     - `TSV` files to start `Sarek` from `prepare_recalibration`, `recalibrate` or `variantcalling` steps for a specific sample.
 
-### TSV files with `--skip_markduplicates`
+### CSV files with `--skip_markduplicates`
 
 > **WARNING** Only with [`--skip_markduplicates`](usage.md#--skip_markduplicates)
 
@@ -159,7 +163,7 @@ For all samples:
 - `mapped_[SAMPLE].tsv`, `mapped_no_duplicates_marked_[SAMPLE].tsv` and `recalibrated_[SAMPLE].tsv`
     - `TSV` files to start `Sarek` from `prepare_recalibration`, `recalibrate` or `variantcalling` steps for a specific sample.
 
-### TSV files with `--sentieon`
+### CSV files with `--sentieon`
 
 > **WARNING** Only with [`--sentieon`](usage.md#--sentieon)