Cleaned up docs

Author: apeltzer

docs/usage.md

@@ -265,14 +265,6 @@ This is by default set to `false`, but can be turned on to calculate on target m
 
 Can be used to set a path to a BED file (3/6 column format) to calculate capture target efficiency on the fly. Will not be used without `--bedfile` set as parameter.
 
-### `--udg` false
-
-Defines whether Uracil-DNA glycosylase (UDG) treatment was used to repair DNA damage on the sequencing libraries. If set, the parameter is used by downstream tools such as PMDTools to estimate damage only on CpG sites that are left after such a treatment. 
-
-### `--pmd_udg_type` \`half`
-
-If you have UDGhalf treated data (Rohland et al 2016), specify `half` as option to this parameter to use a different model for DNA damage assessment in PMDTools. Specify the parameter with `full` and the DNA damage assesment will use CpG context only. If you don't specify the parameter at all, the library will be treated as UDG-.
-
 ## Step skipping parameters
 
 Some of the steps in the pipeline can be executed optionally. If you specify specific steps to be skipped, there won't be any output related to these modules. 
@@ -412,6 +404,15 @@ Specifies the length of the read start and end to be considered for profile gene
 
 Specifies to run PMDTools for damage based read filtering and assessment of DNA damage in sequencing libraries. By default turned off. 
 
+
+### `--udg` false
+
+Defines whether Uracil-DNA glycosylase (UDG) treatment was used to repair DNA damage on the sequencing libraries. If set, the parameter is used by downstream tools such as PMDTools to estimate damage only on CpG sites that are left after such a treatment. 
+
+### `--pmd_udg_type` \`half`
+
+If you have UDGhalf treated data (Rohland et al 2016), specify `half` as option to this parameter to use a different model for DNA damage assessment in PMDTools. Specify the parameter with `full` and the DNA damage assesment will use CpG context only. If you don't specify the parameter at all, the library will be treated as non UDG treated.
+
 ### `--pmdtools_range`
 
 Specifies the range in which to consider DNA damage from the ends of reads. By default set to `10`.