Hook up parameters to the configuration

conf/modules/purecn.config

@@ -0,0 +1,46 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Config file for defining DSL2 per module options and publishing paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Available keys to override module options:
+        ext.args   = Additional arguments appended to command in module.
+        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
+        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
+        ext.prefix = File name prefix for output files.
+        ext.when   = When to run the module.
+----------------------------------------------------------------------------------------
+*/
+
+//PURECN
+
+process {
+
+    withName: 'PURECN_INTERVALFILE' {
+        ext.args   =  [
+            params.genome ? "--genome ${params.genome}": "",
+        ].join(' ')
+
+        ext.when   = { params.tools && params.tools.split(',').contains('purecn') }
+        publishDir = [
+            mode: params.publish_dir_mode,
+            path: { "${params.outdir}/variant_calling/purecn/${meta.id}/" },
+            pattern: "*{.bed,.txt}"
+        ]
+    }
+
+    withName: 'PURECN_RUN' {
+        ext.args   =  [
+            params.genome ? "--genome ${params.genome}": "",
+            params.purecn_exclude_bed ? "--snp-blacklist ${purecn_exclude_bed}": "",
+            "--post-optmize",
+
+        ].join(' ')
+
+        ext.when   = { params.tools && params.tools.split(',').contains('purecn') }
+        publishDir = [
+            mode: params.publish_dir_mode,
+            path: { "${params.outdir}/variant_calling/purecn/${meta.id}/" },
+            pattern: "*{.rds,.txt,*.csv}"
+        ]
+    }
+}

nextflow.config

@@ -78,6 +78,9 @@ params {
     sentieon_dnascope_pcr_indel_model = 'CONSERVATIVE'
     sentieon_haplotyper_emit_mode     = 'variant' // default value for Sentieon haplotyper
     wes                               = false // Set to true, if data is exome/targeted sequencing data. Used to use correct models in various variant callers
+    purecn_normaldb                   = null // NormalDB generated by PureCN
+    purecn_gatk_pon                   = null // PoN data from GATK used by PureCN to denoise coverage
+
 
     // Annotation
     bcftools_annotations     = null  // No extra annotation file

nextflow_schema.json

@@ -417,6 +417,18 @@
                     "description": "Option for selecting the PCR indel model used by Sentieon Dnascope.",
                     "help_text": "PCR indel model used to weed out false positive indels more or less aggressively. The possible MODELs are: NONE (used for PCR free samples), and HOSTILE, AGGRESSIVE and CONSERVATIVE, in order of decreasing aggressiveness. The default value is CONSERVATIVE.",
                     "pattern": "^(NONE|HOSTILE|AGGRESSIVE|CONSERVATIVE)(?<!,)$"
+                },
+                "purecn_normaldb": {
+                    "type": "string",
+                    "pattern": "^\\S+\\.rds$",
+                    "format": "file-path",
+                    "description": "NormalDB file  generated by PureCN NormalDB.R."
+                },
+                "purecn_gatk_pon": {
+                    "type": "string",
+                    "pattern": "^\\S\\.hdf5$",
+                    "format": "file-path",
+                    "description": "Panel of normals generated by the GATK"
                 }
             }
         },

workflows/sarek/main.nf

@@ -826,7 +826,9 @@ workflow SAREK {
             gc_file,
             rt_file,
             params.joint_mutect2,
-            params.wes
+            params.wes,
+            params.purecn_gatk_pon,
+            params.purecn_normaldb
         )
 
         // POST VARIANTCALLING