Merge pull request #112 from apeltzer/pmd_udg_type

Fix redundant UDG flags

Author: apeltzer

CHANGELOG.md

@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### `Fixed`
 * [#110](https://github.com/nf-core/eager/pull/110) - Fix for [MultiQC Missing Second FastQC report](https://github.com/nf-core/eager/issues/107)
+* [#112](https://github.com/nf-core/eager/pull/112) - Remove [redundant UDG options](https://github.com/nf-core/eager/issues/89)
 
 ## [2.0.3] - 2018-12-09
 

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. 
-
-### `--udg_type "Half"`
-
-If you have UDGhalf treated data (Rohland et al 2016), specify this parameter additionally to `--udg` to use a different model for DNA damage assessment in PMDTools.
-
 ## 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`. 

main.nf

@@ -34,8 +34,6 @@ def helpMessage() {
 
     Input Data Additional Options:
       --snpcapture                  Runs in SNPCapture mode (specify a BED file if you do this!)
-      --udg                         Specify that your libraries are treated with UDG
-      --udg_type                    Specify here if you have UDG half treated libraries, Set to 'Half' in that case
 
     References                      If not specified in the configuration file or you wish to overwrite any of the references.
       --bwa_index                   Path to BWA index
@@ -91,6 +89,7 @@ def helpMessage() {
       --damageprofiler_length       Specify length filter for DamageProfiler
       --damageprofiler_threshold    Specify number of bases to consider for damageProfiler
       --run_pmdtools                Turn on PMDtools
+      --udg_type                    Specify here if you have UDG half treated libraries, Set to 'half' in that case, or 'full' for UDG+. If not set, libraries are set to UDG-.
       --pmdtools_range              Specify range of bases for PMDTools
       --pmdtools_threshold          Specify PMDScore threshold for PMDTools
       --pmdtools_reference_mask     Specify a reference mask for PMDTools
@@ -139,8 +138,7 @@ params.bwa_index = false
 params.seq_dict = false
 params.fasta_index = false
 params.saveReference = false
-params.udg = false 
-params.udg_type = 'Half'
+params.pmd_udg_type = 'half'
 
 params.multiqc_config = "$baseDir/conf/multiqc_config.yaml"
 params.email = false
@@ -965,7 +963,7 @@ process pmdtools {
 
     script:
     //Check which treatment for the libraries was used
-    def treatment = params.udg ? (params.udg_type =='half' ? '--UDGhalf' : '--CpG') : '--UDGminus'
+    def treatment = params.pmd_udg_type ? (params.pmd_udg_type =='half' ? '--UDGhalf' : '--CpG') : '--UDGminus'
     if(params.snpcapture){
         snpcap = (params.pmdtools_reference_mask != '') ? "--refseq ${params.pmdtools_reference_mask}" : ''
         log.info"######No reference mask specified for PMDtools, therefore ignoring that for downstream analysis!"