nf-core · ramprasadn · Nov 13, 2023 · Oct 16, 2023 · Oct 16, 2023 · Oct 16, 2023
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - New parameters to skip qualimap and eklipse (`--skip_qualimap` and `--skip_eklipse`) [#436](https://github.com/nf-core/raredisease/pull/436)
 - Fix "there is no process matching config selector warnings" [#435](https://github.com/nf-core/raredisease/pull/435)
 - New parameters to skip fastqc and haplocheck (`--skip_fastqc` and `--skip_haplocheck`) [#438](https://github.com/nf-core/raredisease/pull/438)
+- CNVnator for copy number variant calling [#438](https://github.com/nf-core/raredisease/pull/434)
 
 ### `Changed`
 

diff --git a/README.md b/README.md
@@ -60,6 +60,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
 - [Manta](https://github.com/Illumina/manta)
 - [TIDDIT's sv](https://github.com/SciLifeLab/TIDDIT)
 - Copy number variant calling:
+  - [CNVnator](https://github.com/abyzovlab/CNVnator)
   - [GATK GermlineCNVCaller](https://github.com/broadinstitute/gatk)
 
 **5. Annotation - SNV:**

diff --git a/conf/modules/call_sv_cnvnator.config b/conf/modules/call_sv_cnvnator.config
@@ -0,0 +1,44 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    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
+----------------------------------------------------------------------------------------
+*/
+
+//
+// cnvnator calling options
+//
+
+process {
+
+    withName: ".*CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST" {
+        tag = { "$meta2.id" }
+        ext.args = { "-his ${params.cnvnator_binsize}" }
+    }
+
+    withName: ".*CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT" {
+        tag = { "$meta2.id" }
+        ext.args = { "-stat ${params.cnvnator_binsize}" }
+    }
+
+    withName: ".*CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION" {
+        tag = { "$meta2.id" }
+        ext.args = { "-partition ${params.cnvnator_binsize}" }
+    }
+
+    withName: ".*CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL" {
+        tag = { "$meta2.id" }
+        ext.args = { "-call ${params.cnvnator_binsize}" }
+    }
+
+    withName: '.*CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:SVDB_MERGE_CNVNATOR' {
+        ext.args   = '--notag --pass_only'
+        ext.prefix = { "${meta.id}_cnvnator" }
+    }
+}
diff --git a/docs/output.md b/docs/output.md
@@ -10,57 +10,61 @@ The directories listed below will be created in the results directory after the
 
 The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
 
-- [Alignment](#alignment)
-  - [Mapping](#mapping)
-    - [Bwa-mem2](#bwa-mem2)
-    - [Sentieon bwa mem](#sentieon-bwa-mem)
-  - [Duplicate marking](#duplicate-marking)
-    - [Picard's MarkDuplicates](#picard-s-markduplicates)
-    - [Sentieon dedup](#sentieon-dedup)
-- [Quality control and reporting](#quality-control-and-reporting)
-  - [Quality control](#quality-control)
-    - [FastQC](#fastqc)
-    - [Mosdepth](#mosdepth)
-    - [Picard tools](#picard-tools)
-    - [Qualimap](#qualimap)
-    - [Sentieon WgsMetricsAlgo](#sention-wgsmetricsalgo)
-    - [TIDDIT's cov and UCSC WigToBigWig](#tiddits-cov-and-ucsc-wigtobigwig)
-  - [Reporting](#reporting)
-    - [MultiQC](#multiqc)
-- [Variant calling - SNV](#variant-calling---snv)
-  - [DeepVariant](#deepvariant)
-  - [Sentieon DNAscope](#sentieon-dnascope)
-- [Variant calling - SV](#variant-calling---sv)
-  - [Manta](#manta)
-  - [TIDDIT sv](#tiddit-sv)
-  - [GATK GermlineCNVCaller - CNV calling](#gatk-germlinecnvcaller---cnv-calling)
-  - [SVDB merge](#svdb-merge)
-- [Variant calling - repeat expansions](#variant-calling---repeat-expansions)
-  - [Expansion Hunter](#expansion-hunter)
-  - [Stranger](#stranger)
-- [Annotation - SNV](#annotation---snv)
-  - [bcftools roh](#bcftools-roh)
-  - [vcfanno](#vcfanno)
-  - [CADD](#cadd)
-  - [VEP](#vep)
-  - [UPD](#upd)
-  - [Chromograph](#chromograph)
-- [Annotation - SV](#annotation---sv)
-  - [SVDB query](#svdb-query)
-  - [VEP](#vep-1)
-- [Mitochondrial analysis](#mitochondrial-analysis)
-  - [Alignment and variant calling](#alignment-and-variant-calling)
-    - [MT deletion script](#mt-deletion-script)
-    - [eKLIPse](#eklipse)
-  - [Annotation:](#annotation-)
-    - [HaploGrep2](#haplogrep2)
-    - [vcfanno](#vcfanno-1)
-    - [CADD](#cadd-1)
-    - [VEP](#vep-2)
-    - [HmtNote](#hmtnote)
-- [Rank variants and filtering](#rank-variants-and-filtering)
-  - [GENMOD](#genmod)
-- [Pipeline information](#pipeline-information)
+- [nf-core/raredisease: Output](#nf-coreraredisease-output)
+  - [Introduction](#introduction)
+  - [Pipeline overview](#pipeline-overview)
+    - [Alignment](#alignment)
+      - [Mapping](#mapping)
+        - [Bwa-mem2](#bwa-mem2)
+        - [Sentieon bwa mem](#sentieon-bwa-mem)
+      - [Duplicate marking](#duplicate-marking)
+        - [Picard's MarkDuplicates](#picards-markduplicates)
+        - [Sentieon Dedup](#sentieon-dedup)
+    - [Quality control and reporting](#quality-control-and-reporting)
+      - [Quality control](#quality-control)
+        - [FastQC](#fastqc)
+        - [Mosdepth](#mosdepth)
+        - [Picard tools](#picard-tools)
+        - [Qualimap](#qualimap)
+        - [Sention WgsMetricsAlgo](#sention-wgsmetricsalgo)
+        - [TIDDIT's cov and UCSC WigToBigWig](#tiddits-cov-and-ucsc-wigtobigwig)
+      - [Reporting](#reporting)
+        - [MultiQC](#multiqc)
+    - [Variant calling - SNV](#variant-calling---snv)
+      - [DeepVariant](#deepvariant)
+      - [Sentieon DNAscope](#sentieon-dnascope)
+    - [Variant calling - SV](#variant-calling---sv)
+      - [Manta](#manta)
+      - [TIDDIT sv](#tiddit-sv)
+      - [GATK GermlineCNVCaller - CNV calling](#gatk-germlinecnvcaller---cnv-calling)
+      - [CNVnator - CNV calling](#cnvnator---cnv-calling)
+      - [SVDB merge](#svdb-merge)
+    - [Variant calling - repeat expansions](#variant-calling---repeat-expansions)
+      - [Expansion Hunter](#expansion-hunter)
+      - [Stranger](#stranger)
+    - [Annotation - SNV](#annotation---snv)
+      - [bcftools roh](#bcftools-roh)
+      - [vcfanno](#vcfanno)
+      - [CADD](#cadd)
+      - [VEP](#vep)
+      - [UPD](#upd)
+      - [Chromograph](#chromograph)
+    - [Annotation - SV](#annotation---sv)
+      - [SVDB query](#svdb-query)
+      - [VEP](#vep-1)
+    - [Mitochondrial analysis](#mitochondrial-analysis)
+      - [Alignment and variant calling](#alignment-and-variant-calling)
+        - [MT deletion script](#mt-deletion-script)
+        - [eKLIPse](#eklipse)
+      - [Annotation:](#annotation)
+        - [HaploGrep2](#haplogrep2)
+        - [vcfanno](#vcfanno-1)
+        - [CADD](#cadd-1)
+        - [Hmtnote](#hmtnote)
+        - [VEP](#vep-2)
+    - [Rank variants and filtering](#rank-variants-and-filtering)
+      - [GENMOD](#genmod)
+    - [Pipeline information](#pipeline-information)
 
 ### Alignment
 
@@ -259,6 +263,10 @@ The pipeline performs variant calling using [Sentieon DNAscope](https://support.
 
 [GATK GermlineCNVCaller](https://github.com/broadinstitute/gatk) is used to identify copy number variants in germline samples given their read counts and a model describing a sample's ploidy. Output vcf files are treated as intermediates and are not placed in the output folder.
 
+#### CNVnator - CNV calling
+
+[CNVnator](https://github.com/abyzovlab/CNVnator) is used to identify copy number variants in germline samples given a bam file. Output vcf files are treated as intermediates and are not placed in the output folder.
+
 #### SVDB merge
 
 [SVDB merge](https://github.com/J35P312/SVDB#merge) is used to merge the variant calls from GATK's GermlineCNVCaller (only if skip_germlinecnvcaller is set to false), Manta, and TIDDIT. Output files are published in the output folder.

diff --git a/modules.json b/modules.json
@@ -80,6 +80,16 @@
                         "git_sha": "aad210ba51500be029740d088b4b4827f6f41509",
                         "installed_by": ["modules"]
                     },
+                    "cnvnator/cnvnator": {
+                        "branch": "master",
+                        "git_sha": "e0fcafde1e74156695fc27e90a6ad6325065e6c5",
+                        "installed_by": ["modules"]
+                    },
+                    "cnvnator/convert2vcf": {
+                        "branch": "master",
+                        "git_sha": "e0fcafde1e74156695fc27e90a6ad6325065e6c5",
+                        "installed_by": ["modules"]
+                    },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
                         "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4",

diff --git a/modules/nf-core/cnvnator/cnvnator/main.nf b/modules/nf-core/cnvnator/cnvnator/main.nf
diff --git a/modules/nf-core/cnvnator/cnvnator/meta.yml b/modules/nf-core/cnvnator/cnvnator/meta.yml
diff --git a/modules/nf-core/cnvnator/convert2vcf/main.nf b/modules/nf-core/cnvnator/convert2vcf/main.nf