nf-core · TCLamnidis · Nov 19, 2021 · Nov 18, 2021 · Nov 18, 2021 · Nov 19, 2021
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,7 +7,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### `Added`
 
- - [#808](https://github.com/nf-core/eager/issues/808) Retain read group information across bam merges. Sample set to Sample name in bwa output RG.
+- [#808](https://github.com/nf-core/eager/issues/808) Retain read group information across bam merges. Sample set to Sample name in bwa output RG.
+- Map and base quality filters prior to genotyping with pileupcaller can now be specified.
 
 ### `Fixed`
 

diff --git a/main.nf b/main.nf
@@ -2488,8 +2488,11 @@ process genotyping_pileupcaller {
   def ssmode = strandedness == "single" ? "--singleStrandMode" : ""
   def bam_list = bam.flatten().join(" ")
   def sample_names = samplename.flatten().join(",")
+  def map_q = params.pileupcaller_min_map_quality
+  def base_q = params.pileupcaller_min_base_quality
+
   """
-  samtools mpileup -B -q 30 -Q 30 ${use_bed} -f ${fasta} ${bam_list} | pileupCaller ${caller} ${ssmode} ${transitions_mode} --sampleNames ${sample_names} ${use_snp} -e pileupcaller.${strandedness}
+  samtools mpileup -B --ignore-RG -q ${map_q} -Q ${base_q} ${use_bed} -f ${fasta} ${bam_list} | pileupCaller ${caller} ${ssmode} ${transitions_mode} --sampleNames ${sample_names} ${use_snp} -e pileupcaller.${strandedness}
   """
 }
 

diff --git a/nextflow.config b/nextflow.config
@@ -174,6 +174,8 @@ params {
   pileupcaller_bedfile = null
   pileupcaller_method = 'randomHaploid'
   pileupcaller_transitions_mode = 'AllSites'
+  pileupcaller_min_map_quality = 30
+  pileupcaller_min_base_quality = 30
   // ANGSD Genotype Likelihoods
   angsd_glmodel = 'samtools'
   angsd_glformat = 'binary'

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -1185,6 +1185,20 @@
                         "SkipTransitions"
                     ]
                 },
+                "pileupcaller_min_map_quality": {
+                    "type": "integer",
+                    "default": 30,
+                    "description": "The minimum mapping quality to be used for genotyping.",
+                    "fa_icon": "fas fa-filter",
+                    "help_text": "The minimum mapping quality to be used for genotyping. Affects the `samtools pileup` output that is used by pileupcaller. Affects `-q` parameter of samtools mpileup."
+                },
+                "pileupcaller_min_base_quality": {
+                    "type": "integer",
+                    "default": 30,
+                    "description": "The minimum base quality to be used for genotyping.",
+                    "fa_icon": "fas fa-filter",
+                    "help_text": "The minimum base quality to be used for genotyping. Affects the `samtools pileup` output that is used by pileupcaller. Affects `-Q` parameter of samtools mpileup."
+                },
                 "angsd_glmodel": {
                     "type": "string",
                     "default": "samtools",
@@ -1641,7 +1655,7 @@
                 "maltextract_percentidentity": {
                     "type": "number",
                     "description": "Minimum percent identity alignments are required to have to be reported. Recommended to set same as MALT parameter.",
-                    "default": 85,
+                    "default": 85.0,
                     "fa_icon": "fas fa-id-card",
                     "help_text": "Minimum percent identity alignments are required to have to be reported. Higher values allows fewer mismatches between read and reference sequence, but therefore will provide greater confidence in the hit. Lower values allow more mismatches, which can account for damage and divergence of a related strain/species to the reference. Recommended to set same as MALT parameter or higher. Default: `85.0`.\n\nOnly when `--metagenomic_tool malt` is also supplied.\n\n> Modifies MaltExtract parameter: `--minPI`"
                 },
@@ -1736,4 +1750,4 @@
             "$ref": "#/definitions/metagenomic_authentication"
         }
     ]
-}
+}