Fix mapDamage command and add support for --seq-length parameter

Author: jfy133

CHANGELOG.md

@@ -7,12 +7,15 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### `Added`
 
+- [#933](https://github.com/nf-core/eager/issues/933) Added support for customising --seq-length in mapDamage rescaling (♥ to @ashildv for requesting)
+
 ### `Fixed`
 
 - Changed endors.py license from GPL to MIT (by @aidaanva)
 - Removed erroneous R2 in single-end example in input TSV of usage docs (by @aidaanva)
 - [#928](https://github.com/nf-core/eager/issues/928) Fixed read group incompatibility by re-adding picard AddOrReplaceReadGroups for MultiVCFAnalyzer (♥ to @aidaanva, @meganemichel for reporting)
 - Fixed edge case of DamageProfiler occasionally requiring FASTA index (♥ to @asmaa-a-abdelwahab for reporting)
+- [#934](https://github.com/nf-core/eager/issues/934) Fixed broken parameter setting in mapDamage2 rescale length (♥ to @ashildv for reporting)
 
 ### `Dependencies`
 

main.nf

@@ -2129,8 +2129,10 @@ process mapdamage_rescaling {
     def base = "${bam.baseName}"
     def singlestranded = strandedness == "single" ? '--single-stranded' : ''
     def size = params.large_ref ? '-c' : ''
+    def rescale_length_3p = params.rescale_length_3p != 0 ? "--rescale-length-3p=${params.rescale_length_3p}" : ""
+    def rescale_length_5p = params.rescale_length_5p != 0 ? "--rescale-length-5p=${params.rescale_length_5p}" : ""
     """
-    mapDamage -i ${bam} -r ${fasta} --rescale --rescale-out ${base}_rescaled.bam --rescale-length-5p ${params.rescale_length_5p} --rescale-length-3p=${params.rescale_length_3p} ${singlestranded}
+    mapDamage -i ${bam} -r ${fasta} --rescale --rescale-out="${base}_rescaled.bam" --seq-length=${params.rescale_seqlength} ${rescale_length_5p} ${rescale_length_3p} ${singlestranded}
     samtools index ${base}_rescaled.bam ${size}
     """
 

nextflow.config

@@ -135,8 +135,9 @@ params {
 
   // mapDamage
   run_mapdamage_rescaling = false
-  rescale_length_5p = 12
-  rescale_length_3p = 12
+  rescale_length_5p = 0
+  rescale_length_3p = 0
+  rescale_seqlength = 12
 
   //Bedtools settings
   run_bedtools_coverage = false 

nextflow_schema.json

@@ -914,18 +914,25 @@
                     "description": "Turn on damage rescaling of BAM files using mapDamage2 to probabilistically remove damage.",
                     "help_text": "Turns on mapDamage2's BAM rescaling functionality. This probablistically replaces Ts back to Cs depending on the likelihood this reference-mismatch was originally caused by damage. If the library is specified to be single stranded, this will automatically use the `--single-stranded` mode.\n\nThis functionality does not have any MultiQC output.\n\n:warning: rescaled libraries will not be merged with non-scaled libraries of the same sample for downstream genotyping, as the model may be different for each library. If you wish to merge these, please do this manually and re-run nf-core/eager using the merged BAMs as input. \n\n> Modifies the `--rescale` parameter of mapDamage2"
                 },
-                "rescale_length_5p": {
+                "rescale_seqlength": {
                     "type": "integer",
                     "default": 12,
+                    "fa_icon": "fas fa-ruler-horizontal",
+                    "description": "Length of read sequence to use from each side for rescaling. Can be overridden by --rescale_length_*p.",
+                    "help_text": "Specify the length from the end of the read that mapDamage should rescale at both ends.\n\n> Modifies the `--seq-length` parameter of mapDamage2."
+                },
+                "rescale_length_5p": {
+                    "type": "integer",
+                    "default": 0,
                     "fa_icon": "fas fa-balance-scale-right",
-                    "description": "Length of read for mapDamage2 to rescale from 5p end.",
-                    "help_text": "Specify the length from the end of the read that mapDamage should rescale.\n\n> Modifies the `--rescale-length-5p` parameter of mapDamage2."
+                    "description": "Length of read for mapDamage2 to rescale from 5p end.  Only used if not 0 otherwise --rescale_seqlength used.",
+                    "help_text": "Specify the length from the end of the read that mapDamage should rescale. Overrides `--rescale_seqlength`.\n\n> Modifies the `--rescale-length-5p` parameter of mapDamage2."
                 },
                 "rescale_length_3p": {
                     "type": "integer",
-                    "default": 12,
+                    "default": 0,
                     "fa_icon": "fas fa-balance-scale-left",
-                    "description": "Length of read for mapDamage2 to rescale from 3p end.",
+                    "description": "Length of read for mapDamage2 to rescale from 3p end. Only used if not 0 otherwise --rescale_seqlength used..",
                     "help_text": "Specify the length from the end of the read that mapDamage should rescale.\n\n> Modifies the `--rescale-length-3p` parameter of mapDamage2."
                 }
             },