nf-core · jemten · Dec 20, 2023 · Nov 14, 2023 · Dec 8, 2023 · Dec 18, 2023
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -16,8 +16,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - 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)
 - A new parameter `svdb_query_bedpedbs` to provide bedpe files as databases for SVDB query [#449](https://github.com/nf-core/raredisease/pull/449)
+- ngsbits samplegender to check sex [#453](https://github.com/nf-core/raredisease/pull/453)
+- New workflow for generating cgh files from SV vcfs for interpretation in the CytosSure interpretation software. Turned off by default [#456](https://github.com/nf-core/raredisease/pull/456/)
 - Fastp to do adapter trimming. It can be skipped using `--skip_fastp` [#457](https://github.com/nf-core/raredisease/pull/457)
-- ngsbits samplegender to check sex [#453] (https://github.com/nf-core/raredisease/pull/453)
 
 ### `Changed`
 

diff --git a/CITATIONS.md b/CITATIONS.md
@@ -134,6 +134,8 @@
 
   > Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics. 2010;26(17):2204-2207. doi:10.1093/bioinformatics/btq351
 
+- [vcf2cytosure](https://github.com/NBISweden/vcf2cytosure)
+
 - [Vcfanno](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0973-5)
 
   > Pedersen BS, Layer RM, Quinlan AR. Vcfanno: fast, flexible annotation of genetic variants. Genome Biol. 2016;17(1):118. doi:10.1186/s13059-016-0973-5

diff --git a/conf/modules/generate_cytosure_files.config b/conf/modules/generate_cytosure_files.config
@@ -0,0 +1,50 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    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
+----------------------------------------------------------------------------------------
+*/
+
+//
+// VCF2Cytosure workflow options
+//
+
+process {
+
+    if ( params.analysis_type != "wes" && !params.skip_vcf2cytosure ) {
+
+        withName: '.*GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE' {
+            ext.args = { '-z 500' }
+            ext.prefix = { "${meta.id}_cov" }
+        }
+
+        withName: '.*GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF' {
+            ext.args = { [
+                "--samples ${meta.id}",
+                '--output-type z',
+                "--exclude 'gnomad_svAF > 0.05'"
+                ].join(' ') }
+            ext.prefix = { ${meta.id} }
+        }
+
+        withName: '.*GENERATE_CYTOSURE_FILES:VCF2CYTOSURE' {
+            ext.args = { [
+                meta.sex.equals('1') ? '--sex male' : '--sex female',
+                '--size 5000',
+                '--maxbnd 5000'
+                ].join(' ') }
+            ext.prefix = { "${meta.id}" }
+            publishDir = [
+                path: { "${params.outdir}/vcf2cytosure" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            ]
+        }
+    }
+}
diff --git a/main.nf b/main.nf
@@ -48,6 +48,7 @@ params.target_bed                     = WorkflowMain.getGenomeAttribute(params,
 params.min_trimmed_length             = WorkflowMain.getGenomeAttribute(params, 'min_trimmed_length')
 params.variant_catalog                = WorkflowMain.getGenomeAttribute(params, 'variant_catalog')
 params.vep_filters                    = WorkflowMain.getGenomeAttribute(params, 'vep_filters')
+params.vcf2cytosure_blacklist         = WorkflowMain.getGenomeAttribute(params, 'vcf2cytosure_blacklist')
 params.vcfanno_resources              = WorkflowMain.getGenomeAttribute(params, 'vcfanno_resources')
 params.vcfanno_toml                   = WorkflowMain.getGenomeAttribute(params, 'vcfanno_toml')
 params.vcfanno_lua                    = WorkflowMain.getGenomeAttribute(params, 'vcfanno_lua')

diff --git a/modules.json b/modules.json
@@ -450,7 +450,8 @@
                     "tiddit/cov": {
                         "branch": "master",
                         "git_sha": "1c90a501d102b800c27697f5ef39a6e217ab1915",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/tiddit/cov/tiddit-cov.diff"
                     },
                     "tiddit/sv": {
                         "branch": "master",
@@ -472,6 +473,12 @@
                         "git_sha": "9b159849d74f0eef251168c81c16da08215bbad5",
                         "installed_by": ["modules"]
                     },
+                    "vcf2cytosure": {
+                        "branch": "master",
+                        "git_sha": "2dba354d7c0a43a1e6d6ce26f408b4936d4ed619",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/vcf2cytosure/vcf2cytosure.diff"
+                    },
                     "vcfanno": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",

diff --git a/modules/nf-core/tiddit/cov/main.nf b/modules/nf-core/tiddit/cov/main.nf
diff --git a/modules/nf-core/tiddit/cov/meta.yml b/modules/nf-core/tiddit/cov/meta.yml
diff --git a/modules/nf-core/tiddit/cov/tiddit-cov.diff b/modules/nf-core/tiddit/cov/tiddit-cov.diff
diff --git a/modules/nf-core/vcf2cytosure/environment.yml b/modules/nf-core/vcf2cytosure/environment.yml
diff --git a/modules/nf-core/vcf2cytosure/main.nf b/modules/nf-core/vcf2cytosure/main.nf
diff --git a/modules/nf-core/vcf2cytosure/meta.yml b/modules/nf-core/vcf2cytosure/meta.yml
diff --git a/modules/nf-core/vcf2cytosure/vcf2cytosure.diff b/modules/nf-core/vcf2cytosure/vcf2cytosure.diff
diff --git a/nextflow.config b/nextflow.config
@@ -33,6 +33,7 @@ params {
     skip_snv_annotation        = false
     skip_sv_annotation         = false
     skip_mt_annotation         = false
+    skip_vcf2cytosure          = true
     skip_vep_filter            = false
     gens_switch                = false
     cadd_resources             = null
@@ -304,6 +305,7 @@ includeConfig 'conf/modules/call_repeat_expansions.config'
 includeConfig 'conf/modules/call_snv.config'
 includeConfig 'conf/modules/call_structural_variants.config'
 includeConfig 'conf/modules/convert_mt_bam_to_fastq.config'
+includeConfig 'conf/modules/generate_cytosure_files.config'
 includeConfig 'conf/modules/gens.config'
 includeConfig 'conf/modules/peddy_check.config'
 includeConfig 'conf/modules/prepare_references.config'

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -321,6 +321,14 @@
                     "help_text": "Should be Stranger's extended JSON as described at https://github.com/Clinical-Genomics/stranger/blob/master/stranger/resources/variant_catalog_grch37.json. This file is used by both ExpansionHunter and Stranger",
                     "fa_icon": "fas fa-file"
                 },
+                "vcf2cytosure_blacklist": {
+                    "type": "string",
+                    "help_text": "Optional file to blacklist regions for VCF2cytosure",
+                    "pattern": "^\\S+\\.bed$",
+                    "format": "file-path",
+                    "fa_icon": "fas fa-file",
+                    "description": "Path to vcf2cytosure blacklist file"
+                },
                 "vcfanno_resources": {
                     "type": "string",
                     "exists": true,
@@ -443,6 +451,13 @@
                     "description": "Specifies whether or not to skip annotate structural variant subworkflow.",
                     "fa_icon": "fas fa-toggle-on"
                 },
+                "skip_vcf2cytosure": {
+                    "type": "boolean",
+                    "default": true,
+                    "description": "Specifies whether or not to skip the vcf2cytosure subworkflow",
+                    "help_text": "vcf2cytosure can generate CGH files from a structural variant VCF file that can be analysed in the CytoSure interpretation software. Cut-offs for allele frequencies and bin sizes can be modified in the config file. Turned off by default.",
+                    "fa_icon": "fas fa-toggle-on"
+                },
                 "skip_vep_filter": {
                     "type": "boolean",
                     "description": "Specifies whether or not to filter results based on a list of candidate genes specified in 'vep_filters'.",