Merge pull request #69 from nf-core/update-usage

Update documentation in usage.md

docs/usage.md

@@ -48,6 +48,17 @@ samplesheet. The supported analysis types for each workflow are listed below.
 
 <sub><sup>\*</sup> Supported analyses relate to the TSO500 panel only</sub>
 
+:::note
+
+The default settings of `oncoanalyser` will accommodate typical sequencing depths for sample inputs and each individual
+tool is generally sequencing depth agnostic. However, variant calling is optimised for 100x tumor and 40x normal when
+invoked in `wgts` mode and expects sparse high-depth read data characteristic of panel sequencing when run in `targeted`
+mode. For atypical input sequence data you may consult the [hmftools
+documentation](https://github.com/hartwigmedical/hmftools) and [configure](#custom-tool-arguments) `oncoanalyser`
+accordingly.
+
+:::
+
 ## Samplesheet
 
 A samplesheet that contains information of each input in CSV format is needed to run `oncoanalyser`. The required input
@@ -320,7 +331,7 @@ params {
 To use these hmftools resource file overrides in `oncoanalyser` the local bundle directory must be provided with
 `--ref_data_hmf_data_path`.
 
-#### Customise other data
+#### Customising other data
 
 The path or URI to the VIRUSBreakend database can also be explicitly set with `--ref_data_virusbreakenddb_path`. There
 are additional arguments to manually set various other reference data files, please review the parameters documentation