Merge pull request #708 from nf-core/pmdtools-extension

Pmdtools extension

Author: apeltzer

CHANGELOG.md

@@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### `Added`
 
+- [#349](https://github.com/nf-core/eager/issues/349) - Added option enabling platypus formatted output of pmdtools misincorporation frequencies.
+
 ### `Fixed`
 
 - [#707](https://github.com/nf-core/eager/pull/707) - Fix typo in UnifiedGenotyper IndelRealigner command

main.nf

@@ -2042,14 +2042,15 @@ process pmdtools {
         snpcap = ''
     }
     def size = params.large_ref ? '-c' : ''
+    def platypus = params.pmdtools_platypus ? '--platypus' : ''
     """
     #Run Filtering step 
-    samtools calmd -b $bam $fasta | samtools view -h - | pmdtools --threshold ${params.pmdtools_threshold} $treatment $snpcap --header | samtools view -@ ${task.cpus} -Sb - > "${libraryid}".pmd.bam
+    samtools calmd -b ${bam} ${fasta} | samtools view -h - | pmdtools --threshold ${params.pmdtools_threshold} ${treatment} ${snpcap} --header | samtools view -@ ${task.cpus} -Sb - > "${libraryid}".pmd.bam
     
     #Run Calc Range step
     ## To allow early shut off of pipe: https://github.com/nextflow-io/nextflow/issues/1564
     trap 'if [[ \$? == 141 ]]; then echo "Shutting samtools early due to -n parameter" && samtools index ${libraryid}.pmd.bam ${size}; exit 0; fi' EXIT
-    samtools calmd -b $bam $fasta | samtools view -h - | pmdtools --deamination --range ${params.pmdtools_range} $treatment $snpcap -n ${params.pmdtools_max_reads} > "${libraryid}".cpg.range."${params.pmdtools_range}".txt
+    samtools calmd -b ${bam} ${fasta} | samtools view -h - | pmdtools --deamination ${platypus} --range ${params.pmdtools_range} ${treatment} ${snpcap} -n ${params.pmdtools_max_reads} > "${libraryid}".cpg.range."${params.pmdtools_range}".txt
     
     echo "Running indexing"
     samtools index ${libraryid}.pmd.bam ${size}

nextflow.config

@@ -118,6 +118,7 @@ params {
   pmdtools_threshold = 3
   pmdtools_reference_mask = ''
   pmdtools_max_reads = 10000
+  pmdtools_platypus = false
 
   // mapDamage
   run_mapdamage_rescaling = false

nextflow_schema.json

@@ -813,6 +813,12 @@
                     "fa_icon": "fas fa-greater-than-equal",
                     "help_text": "The maximum number of reads used for damage assessment in PMDtools. Can be used to significantly reduce the amount of time required for damage assessment in PMDTools. Note that a too low value can also obtain incorrect results.\n\n> Modifies PMDTools parameter: `-n`"
                 },
+                "pmdtools_platypus": {
+                    "type": "boolean",
+                    "description": "Append big list of base frequencies for platypus to output.",
+                    "fa_icon": "fas fa-power-off",
+                    "help_text": "Enables the printing of a wider list of base frequencies used by platypus as an addition to the output base misincorporation frequency table. By default turned off.\n"
+                },
                 "run_mapdamage_rescaling": {
                     "type": "boolean",
                     "fa_icon": "fas fa-map",