Merge pull request #351 from jfy133/damageprofiler-yaxis

Damageprofiler yaxis

Author: jfy133

.github/workflows/ci.yml

@@ -32,7 +32,7 @@ jobs:
           docker pull nfcore/eager:dev && docker tag nfcore/eager:dev nfcore/eager:dev
       - name: Extract branch name
         shell: bash
-        run: echo "::set-env name=RUN_NAME::`echo ${GITHUB_REPOSITORY//\//_}`-`echo ${GITHUB_HEAD_REF//\//@} | rev | cut -f1 -d@ | rev`-${{ github.event_name }}-`echo ${GITHUB_SHA} | cut -c1-6`"
+        run: echo "::set-env name=RUN_NAME::`echo ${GITHUB_REPOSITORY//\//_}`-${{ github.event_name }}-`echo ${GITHUB_SHA} | cut -c1-6`"
         id: extract_branch
       - name: Determine tower usage
         shell: bash

CHANGELOG.md

@@ -25,6 +25,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 * [#286](https://github.com/nf-core/eager/issues/286) - Adds pipeline-specific profiles (loaded from nf-core configs)
 * [#310](https://github.com/nf-core/eager/issues/310) - Generalises base.config
 * [#326](https://github.com/nf-core/eager/pull/326) - Add Biopython and [xopen](https://github.com/marcelm/xopen/) dependencies
+* [#336](https://github.com/nf-core/eager/issues/336) - Change default Y-axis maximum value of DamageProfiler to 30% to match popular (but slower) mapDamage, and allow user to set their own value.
 * [#352](https://github.com/nf-core/eager/pull/352) - Add social preview image
 
 ### `Fixed`

docs/usage.md

@@ -629,6 +629,10 @@ Specifies the length filter for DamageProfiler. By default set to `100`.
 
 Specifies the length of the read start and end to be considered for profile generation in DamageProfiler. By default set to `15` bases.
 
+#### `--damageprofiler_yaxis`
+
+Specifies what the maximum misincorporation frequency should be displayed as, in the DamageProfiler damage plot. This is set to `0.30` (i.e. 30%) by default as this matches the popular [mapDamage2.0](https://ginolhac.github.io/mapDamage) program. However, the default behaviour of DamageProfiler is to 'autoscale' the y-axis maximum to zoom in on any _possible_ damage that may occur (e.g. if the damage is about 10%, the highest value on the y-axis would be set to 0.12). This 'autoscale' behaviour can be turned on by specifying the number to `0`. Default: `0.30`.
+
 #### `--run_pmdtools`
 
 Specifies to run PMDTools for damage based read filtering and assessment of DNA damage in sequencing libraries. By default turned off.

main.nf

@@ -104,7 +104,8 @@ def helpMessage() {
 
     (aDNA) Damage Analysis
       --damageprofiler_length       Specify length filter for DamageProfiler
-      --damageprofiler_threshold    Specify number of bases to consider for damageProfiler
+      --damageprofiler_threshold    Specify number of bases to consider for damageProfiler (e.g. on damage plot). Default: 15
+      --damageprofiler_yaxis        Specify the maximum misincorporation frequency that should be displayed on damage plot. Set to 0 to 'autoscale'. Default: 0.30 
       --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
@@ -1519,7 +1520,7 @@ process damageprofiler {
     script:
     base = "${bam.baseName}"
     """
-    damageprofiler -i $bam -r $fasta -l ${params.damageprofiler_length} -t ${params.damageprofiler_threshold} -o . 
+    damageprofiler -i $bam -r $fasta -l ${params.damageprofiler_length} -t ${params.damageprofiler_threshold} -o . -yaxis_damageplot ${params.damageprofiler_yaxis}
     """
 }
 

nextflow.config

@@ -81,6 +81,7 @@ params {
   //DamageProfiler settings
   damageprofiler_length = 100
   damageprofiler_threshold = 15
+  damageprofiler_yaxis = 0.30
 
   //DeDuplication settings
   dedupper = 'dedup' //default value dedup