Add Parabricks DeepVariant module

CHANGELOG.md

@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Interval parameter in the default retroseq call [#717](https://github.com/nf-core/raredisease/pull/717)
 - Tests for call_repeat_expansions and qc_bam subworkflows [#713](https://github.com/nf-core/raredisease/pull/713)
+- Parabricks DeepVariant as an optional variant caller [#724](https://github.com/nf-core/raredisease/pull/724)
 - Feature to subsample mitochondrial alignments based on number of reads [#748](https://github.com/nf-core/raredisease/pull/748)
 - Functionality to generate coverage information using Sambamba depth [#752](https://github.com/nf-core/raredisease/pull/752)
 
@@ -41,6 +42,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | htslib                              | 1.20        | 1.21        |
 | mosdepth                            | 0.3.8       | 0.3.10      |
 | ngs-bits                            | 2023_02     | 2024_11     |
+| pbrun                               |             | 4.5.1-1     |
 | gatk4/determinegermlinecontigploidy | 4.5.0.0     | 4.6.2.0     |
 | gatk4/germlinecnvcaller             | 4.5.0.0     | 4.6.2.0     |
 | gens-preproc                        | 1.0.11      | 1.1.2       |

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

@@ -323,6 +323,11 @@
                         "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
                         "installed_by": ["modules"]
                     },
+                    "parabricks/deepvariant": {
+                        "branch": "master",
+                        "git_sha": "e824d95384679ea50c6c49aae9851160de80a301",
+                        "installed_by": ["modules"]
+                    },
                     "peddy": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",