Add Parabricks DeepVariant module

Author: HudoGriz

CHANGELOG.md

@@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Added`
 
 - Interval parameter in the default retroseq call [#717](https://github.com/nf-core/raredisease/pull/717)
+- Parabricks DeepVariant as an optional variant caller
 
 ### `Changed`
 
@@ -26,9 +27,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Tool updates
 
-| Tool | Old version | New version |
-| ---- | ----------- | ----------- |
-|      |             |             |
+| Tool  | Old version | New version |
+| ----- | ----------- | ----------- |
+| pbrun |             | 4.5.1-1     |
 
 ## 2.6.0 - Cacofonix [2025-06-25]
 

conf/modules/call_snv_deepvariant_parabricks.config

@@ -0,0 +1,59 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    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            = Conditional clause
+----------------------------------------------------------------------------------------
+*/
+
+//
+// SNV calling options - parabricks deepvariant
+//
+
+process {
+
+    withName: '.*CALL_SNV_DEEPVARIANT_PARABRICKS:.*' {
+        ext.when = params.variant_caller.equals("parabricks_deepvariant")
+    }
+
+    withName: '.*CALL_SNV_DEEPVARIANT_PARABRICKS:PARABRICKS_DEEPVARIANT' {
+        ext.args = { [
+            '--gvcf',
+            params.analysis_type.toUpperCase() == 'WES' ? '--use-wes-model' : '',
+            (meta.sex == 1) ?
+                (params.genome == 'GRCh37' ? '--haploid-contigs X,Y' : '--haploid-contigs chrX,chrY')
+                : ''
+        ].findAll { it }.join(' ').trim() }
+
+        ext.prefix = { "${meta.id}_parabricks_deepvar" }
+
+        label = 'process_gpu'
+    }
+
+    withName: '.*CALL_SNV_DEEPVARIANT_PARABRICKS:GLNEXUS' {
+        ext.args = '--config DeepVariant_unfiltered'
+    }
+
+    withName: '.*CALL_SNV_DEEPVARIANT_PARABRICKS:SPLIT_MULTIALLELICS_PB' {
+        ext.args = '--output-type z --multiallelics -both'
+    }
+
+    withName: '.*CALL_SNV_DEEPVARIANT_PARABRICKS:REMOVE_DUPLICATES_PB' {
+        ext.args = '--output-type z --rm-dup none'
+        ext.prefix = { "${meta.id}_split_rmdup" }
+    }
+
+    withName: '.*CALL_SNV_DEEPVARIANT_PARABRICKS:ADD_VARCALLER_TO_BED' {
+        ext.args2   = '-s 1 -b 2 -e 3'
+    }
+
+    withName: '.*CALL_SNV_DEEPVARIANT_PARABRICKS:BCFTOOLS_ANNOTATE' {
+        ext.args = "-c CHROM,FROM,TO,FOUND_IN --output-type z"
+        ext.prefix = { "${meta.id}_split_rmdup_info" }
+    }
+}

modules.json

@@ -318,6 +318,11 @@
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
+                    "parabricks/deepvariant": {
+                        "branch": "master",
+                        "git_sha": "e824d95384679ea50c6c49aae9851160de80a301",
+                        "installed_by": ["modules"]
+                    },
                     "peddy": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",