Feat/vqsr

conf/modules.config

@@ -21,6 +21,7 @@ def enableOutput(state) {
         "add_ped": params.add_ped,
         "normalize": params.normalize,
         "filter": params.filter,
+        "vqsr": params.vqsr,
         "original": true
     ]
 
@@ -257,6 +258,50 @@ process {
                     ] // SAVE
                 }
 
+                if(params.vqsr) {
+                    withName: "^.*VCF_VQSR_GATK4:GATK4_VARIANTRECALIBRATOR_SNPS" {
+                        // -an DP => This option is not advised for WES runs, see if this can somehow still be added to WGS runs
+                        ext.args = [
+                            "-an QD",
+                            "-an MQ",
+                            "-an MQRankSum",
+                            "-an ReadPosRankSum",
+                            "-an FS",
+                            "-an SOR",
+                            "-mode SNP"
+                        ].join(" ")
+                    }
+
+                    withName: "^.*VCF_VQSR_GATK4:GATK4_VARIANTRECALIBRATOR_INDELS" {
+                        // -an DP => This option is not advised for WES runs, see if this can somehow still be added to WGS runs
+                        ext.args = [
+                            "-an QD",
+                            "-an MQRankSum",
+                            "-an ReadPosRankSum",
+                            "-an FS",
+                            "-an SOR",
+                            "-mode INDEL"
+                        ].join(" ")
+                    }
+
+                    withName: "^.*VCF_VQSR_GATK4:GATK4_APPLYVQSR_SNPS" {
+                        ext.args   = "--truth-sensitivity-filter-level 99.9 -mode SNP"
+                        ext.prefix = { "${meta.id}_snp" }
+                    }
+
+                    withName: "^.*VCF_VQSR_GATK4:GATK4_APPLYVQSR_INDELS" {
+                        ext.args   = "--truth-sensitivity-filter-level 99.9 -mode INDEL"
+                        ext.prefix = enableOutput("vqsr") ? final_prefix : { "${meta.id}.vqsr" }
+                        publishDir = [
+                            enabled: enableOutput("vqsr"),
+                            overwrite: true,
+                            path: final_output,
+                            mode: params.publish_dir_mode,
+                            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                        ] // SAVE
+                    }
+                }
+
                 if(params.filter){
                     withName: "^.*CRAM_CALL_GENOTYPE_GATK4:VCF_FILTER_BCFTOOLS:FILTER_1\$" {
                         ext.prefix = { "${meta.id}_filtered_snps" }

main.nf

@@ -39,6 +39,14 @@ params.alphamissense        = getGenomeAttribute('alphamissense')
 params.alphamissense_tbi    = getGenomeAttribute('alphamissense_tbi')
 params.vcfanno_resources    = getGenomeAttribute('vcfanno_resources')
 params.vcfanno_config       = getGenomeAttribute('vcfanno_config')
+params.hapmap               = getGenomeAttribute('hapmap')           
+params.hapmap_tbi           = getGenomeAttribute('hapmap_tbi')
+params.omni_1000G            = getGenomeAttribute('omni_1000G')
+params.omni_1000G_tbi        = getGenomeAttribute('omni_1000G_tbi')
+params.snps_1000G            = getGenomeAttribute('snps_1000G')
+params.snps_1000G_tbi        = getGenomeAttribute('snps_1000G_tbi')
+params.indels_1000G          = getGenomeAttribute('indels_1000G')
+params.indels_1000G_tbi      = getGenomeAttribute('indels_1000G_tbi')
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -80,6 +88,24 @@ if (params.output_suffix && callers.size() > 1) {
     error("Cannot use --output_suffix with more than one caller")
 }
 
+if(params.vqsr) {
+    if(!params.hapmap || !params.hapmap_tbi) {
+        error("Please provide --hapmap and --hapmap_tbi when using --vqsr")
+    }
+    if(!params.omni_1000G || !params.omni_1000G_tbi) {
+        error("Please provide --omni_1000G and --omni_1000G_tbi when using --vqsr")
+    }
+    if(!params.snps_1000G || !params.snps_1000G_tbi) {
+        error("Please provide --snps_1000G and --snps_1000G_tbi when using --vqsr")
+    }
+    if(!params.indels_1000G || !params.indels_1000G_tbi) {
+        error("Please provide --indels_1000G and --indels_1000G_tbi when using --vqsr")
+    }
+    if(!params.dbsnp || !params.dbsnp_tbi) {
+        error("Please provide --dbsnp and --dbsnp_tbi when using --vqsr")
+    }    
+}
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     CONFIG FILES
@@ -150,6 +176,14 @@ workflow NFCMGG_GERMLINE {
         params.automap_repeats,
         params.automap_panel,
         params.outdir,
+        params.hapmap,
+        params.hapmap_tbi,
+        params.omni_1000G,
+        params.omni_1000G_tbi,
+        params.snps_1000G,
+        params.snps_1000G_tbi,
+        params.indels_1000G,
+        params.indels_1000G_tbi,
 
         // Boolean inputs
         params.dragstr,
@@ -169,6 +203,7 @@ workflow NFCMGG_GERMLINE {
         params.vep_mastermind,
         params.vep_eog,
         params.vep_alphamissense,
+        params.vqsr,
 
         // Value inputs
         params.genome,

modules.json

@@ -79,6 +79,11 @@
                         "installed_by": ["vcf_annotate_ensemblvep_snpeff"],
                         "patch": "modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff"
                     },
+                    "gatk4/applyvqsr": {
+                        "branch": "master",
+                        "git_sha": "cee8fe33d3ef1a220dee67dac75a32f7c872f63f",
+                        "installed_by": ["modules"]
+                    },
                     "gatk4/calibratedragstrmodel": {
                         "branch": "master",
                         "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
@@ -111,6 +116,11 @@
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/gatk4/haplotypecaller/gatk4-haplotypecaller.diff"
                     },
+                    "gatk4/variantrecalibrator": {
+                        "branch": "master",
+                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
+                        "installed_by": ["modules"]
+                    },
                     "gawk": {
                         "branch": "master",
                         "git_sha": "dc3527855e7358c6d8400828754c0caa5f11698f",