Add mutect2 as a caller

.nf-core.yml

@@ -41,4 +41,4 @@ template:
   skip_features:
     - fastqc
     - is_nfcore
-  version: 1.13.6
+  version: 1.14.0dev

CHANGELOG.md

@@ -3,6 +3,23 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v1.14.0dev
+
+### New features
+
+- Added a new caller: `GATK4_MUTECT2` followed by `GATK4_FILTERMUTECTCALLS`. Pass `mutect2` to the `--callers` parameter to use it.
+
+### Changes
+
+- Check that the VCF contains enough variants before running automap (it needs to have at least 10000 variants)
+
+### Parameters
+
+| Old | New                      |
+| --- | ------------------------ |
+|     | `--panel_of_normals`     |
+|     | `--panel_of_normals_tbi` |
+
 ## v1.13.6
 
 - Revert the default configs base to the nf-core configs in preparation of converting nf-cmgg/configs to a private repo

assets/multiqc_config.yml

@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-cmgg/smallvariants/releases/tag/1.13.6" target="_blank">nf-cmgg/smallvariants</a> analysis pipeline.
+  This report has been generated by the <a href="https://github.com/nf-cmgg/smallvariants/tree/dev" target="_blank">nf-cmgg/smallvariants</a> analysis pipeline.
 report_section_order:
   "nf-cmgg-smallvariants-methods-description":
     order: -1000

conf/modules.config

@@ -72,11 +72,11 @@ process {
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     */
 
-    withName: "^.*CRAM_CALL_GATK4:GATK4_CALIBRATEDRAGSTRMODEL\$" {
+    withName: "^.*CRAM_CALL_HAPLOTYPECALLER:GATK4_CALIBRATEDRAGSTRMODEL\$" {
         ext.args    = "--parallel"
     }
 
-    withName: "^.*CRAM_CALL_GATK4:GATK4_HAPLOTYPECALLER\$" {
+    withName: "^.*CRAM_CALL_HAPLOTYPECALLER:GATK4_HAPLOTYPECALLER\$" {
         time        = { 16.h  * task.attempt }
         ext.prefix  = {"${meta.id}.g"}
         ext.args    = {
@@ -91,12 +91,12 @@ process {
         }
     }
 
-    withName: "^.*CRAM_CALL_GATK4:VCF_CONCAT_BCFTOOLS:BCFTOOLS_CONCAT\$" {
+    withName: "^.*CRAM_CALL_HAPLOTYPECALLER:VCF_CONCAT_BCFTOOLS:BCFTOOLS_CONCAT\$" {
         ext.prefix = { "${meta.id}.${meta.caller}.g" }
         ext.args   = '--allow-overlaps --output-type z --write-index=tbi'
     }
 
-    withName: "^.*CRAM_CALL_GATK4:BCFTOOLS_STATS\$" {
+    withName: "^.*CRAM_CALL_HAPLOTYPECALLER:BCFTOOLS_STATS\$" {
         ext.prefix = { "${meta.id}.${meta.caller}" }
     }
 
@@ -204,6 +204,44 @@ process {
         ext.prefix = {"${meta.id}.concat"}
     }
 
+    /*
+    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+        MUTECT2
+    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    */
+
+    withName: "^.*CRAM_CALL_MUTECT2:GATK4_MUTECT2\$" {
+        time        = { 16.h  * task.attempt }
+        ext.args    = [
+            "--annotation ClippingRankSumTest",
+            "--annotation DepthPerSampleHC",
+            "--annotation MappingQualityRankSumTest",
+            "--annotation MappingQualityZero",
+            "--annotation QualByDepth",
+            "--annotation ReadPosRankSumTest",
+            "--annotation RMSMappingQuality",
+            "--annotation FisherStrand",
+            "--annotation MappingQuality",
+            "--annotation DepthPerAlleleBySample",
+            "--annotation Coverage",
+            "--read-validation-stringency LENIENT",
+            "--interval-set-rule INTERSECTION",
+            "--max-reads-per-alignment-start 0",
+            "--initial-tumor-lod 0",
+            "--tumor-lod-to-emit 0",
+            "--min-base-quality-score 20"
+        ].join(" ")
+    }
+
+    withName: "^.*CRAM_CALL_MUTECT2:GATK4_FILTERMUTECTCALLS\$" {
+        ext.prefix = {"${meta.id}.filtered"}
+    }
+
+    withName: "^.*CRAM_CALL_MUTECT2:VCF_CONCAT_BCFTOOLS:BCFTOOLS_CONCAT\$" {
+        ext.args   = '--allow-overlaps --output-type z --write-index=tbi'
+        ext.prefix = {"${meta.id}.concat"}
+    }
+
     /*
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
         FILTER

main.nf

@@ -318,6 +318,12 @@ params {
 
     // A semicolon-seperated list of resource files for VCFanno, please also supply their indices using this parameter.
     vcfanno_resources: String? = getGenomeAttribute('vcfanno_resources', params.genomes, params.genome)
+
+    // Path to the panel of normals VCF file.
+    panel_of_normals: Path? = getGenomeAttribute('panel_of_normals', params.genomes, params.genome)
+
+    // Path to the index of the panel of normals VCF file.
+    panel_of_normals_tbi: Path? = getGenomeAttribute('panel_of_normals_tbi', params.genomes, params.genome)
 }
 
 workflow {
@@ -333,12 +339,16 @@ workflow {
     // Check for dependencies between parameters
     //
 
-    def List<String> available_callers = ["haplotypecaller", "vardict", "elprep"]
+    def List<String> available_callers = ["haplotypecaller", "vardict", "elprep", "mutect2"]
 
     if(params.dbsnp_tbi && !params.dbsnp){
         error("Please specify the dbsnp VCF with --dbsnp VCF")
     }
 
+    if(params.panel_of_normals_tbi && !params.panel_of_normals){
+        error("Please specify the panel of normals VCF with --panel_of_normals VCF")
+    }
+
     if (params.annotate) {
         // Check if a genome is given
         if (!params.genome) { error("A genome should be supplied for annotation (use --genome)") }
@@ -358,7 +368,7 @@ workflow {
 
     def callers = params.callers.tokenize(",")
     callers.each { caller ->
-        if(!(caller in available_callers)) { error("\"${caller}\" is not a supported callers please use one or more of these instead: ${available_callers.join(', ')}") }
+        if(!(caller in available_callers)) { error("\"${caller}\" is not a supported caller please use one or more of these instead: ${available_callers.join(', ')}") }
     }
 
     /*
@@ -432,6 +442,8 @@ workflow {
         params.elsites,
         params.msi_baseline,
         params.updio_regions,
+        params.panel_of_normals,
+        params.panel_of_normals_tbi,
 
         // Boolean inputs
         params.dragstr,

modules.json

@@ -102,6 +102,11 @@
                         "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["modules"]
                     },
+                    "gatk4/filtermutectcalls": {
+                        "branch": "master",
+                        "git_sha": "d5de7a949aa84689f4098c958f05733a6c3804f5",
+                        "installed_by": ["modules"]
+                    },
                     "gatk4/genomicsdbimport": {
                         "branch": "master",
                         "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
@@ -117,6 +122,11 @@
                         "git_sha": "b73338eca19d798eb0ef6ed112ef4d27a30d2871",
                         "installed_by": ["modules"]
                     },
+                    "gatk4/mutect2": {
+                        "branch": "master",
+                        "git_sha": "6ef220fd9252b42fb3c50348bbdbcb6246730686",
+                        "installed_by": ["modules"]
+                    },
                     "gawk": {
                         "branch": "master",
                         "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",