Fully implement annotation

assets/vcfanno/1KGP_3202.toml

@@ -0,0 +1,5 @@
+[[annotation]]
+file="1KGP_3202.gatksv_svtools_novelins.freeze_V3.wAF.GRCh38.vcf.gz"
+fields=["AF"]
+ops=["self"]
+names=["AF_1000G"]

assets/vcfanno/CREs_v1.toml

@@ -0,0 +1,5 @@
+[[annotation]]
+file="CREs.v1.coordinates.bed.gz"
+columns=[4]
+ops=["self"]
+names=["CRE_Gene_name"]

assets/vcfanno/IRD_v9.toml

@@ -0,0 +1,5 @@
+[[annotation]]
+file="IRD.v9.coordinates.bed"
+columns=[4]
+ops=["self"]
+names=["IRD_Gene_name"]

assets/vcfanno/RetNetCNV_v1.toml

@@ -0,0 +1,5 @@
+[[annotation]]
+file="RetNetCNV.v1.coordinates.bed"
+columns=[4]
+ops=["self"]
+names=["RetNetCNV_Gene_name"]

assets/vcfanno/RetNet_v6.toml

@@ -0,0 +1,5 @@
+[[annotation]]
+file="RetNet.v6.coordinates.bed"
+columns=[4]
+ops=["self"]
+names=["RetNet_Gene_name"]

assets/vcfanno/all_v8.toml

@@ -0,0 +1,5 @@
+[[annotation]]
+file="ALL.wgs.mergedSV.v8.20130502.svs.genotypes.GRCh38.vcf.gz"
+fields=["AF"]
+ops=["self"]
+names=["AF_ALLv8"]

assets/vcfanno/annotsv.toml

@@ -0,0 +1,5 @@
+[[annotation]]
+file="annotsv_annotated.vcf.gz"
+fields=["AnnotSV_ID", "Samples_ID", "Gene_name", "Gene_count", "Cosmic_ID", "RE_gene", "CytoBand", "OMIM_ID", "GnomAD_pLI", "ExAC_pLI", "ACMG_class", "AnnotSV_ranking_score", "AnnotSV_ranking_criteria"]
+names=["AnnotSV_ID", "Samples_ID", "Gene_name", "Gene_count", "Cosmic_ID", "RE_gene", "CytoBand", "OMIM_ID", "GnomAD_pLI", "ExAC_pLI", "ACMG_class", "AnnotSV_ranking_score", "AnnotSV_ranking_criteria"]
+ops=["self", "self", "self", "self", "self", "self", "self", "self", "self", "self", "self", "self", "self"]

assets/vcfanno/dbVar.toml

@@ -0,0 +1,5 @@
+[[annotation]]
+file="dbVar.GRCh38.variant_call.all.vcf.gz"
+fields=["AF"]
+ops=["self"]
+names=["AF_dbVar"]

assets/vcfanno/goNL_AF_genotyped_SVs.toml

@@ -0,0 +1,5 @@
+[[annotation]]
+file="GoNL_AF_genotyped_SVs.v6.1.20161013.vcf.gz"
+fields=["AF"]
+ops=["self"]
+names=["AF_goNL"]

assets/vcfanno/nstd166.toml

@@ -0,0 +1,5 @@
+[[annotation]]
+file="nstd166.GRCh38.variant_call.vcf.gz"
+fields=["AF","DBVARID","REGIONID","CLNSIG","CLNACC"]
+ops=["self","self","self","self","self"]
+names=["AF_gnomAD","DBVARID","REGIONID","CLNSIG","CLNACC"]

assets/vcfanno/retina_scale.toml

@@ -0,0 +1,6 @@
+[[annotation]]
+file="retina_scale_res25000_win250000.TADboundaries.bed"
+columns=[4]
+#TODO: define the name and ops here
+#names=["RetNetCNV_Gene_name"]
+#ops=["self"]

assets/vcfanno/rpe_scale.toml

@@ -0,0 +1,6 @@
+[[annotation]]
+file="rpe_scale_res25000_win250000.TADboundaries.bed"
+columns=[4]
+#TODO: define the name and ops here
+#names=["RetNetCNV_Gene_name"]
+#ops=["self"]

conf/modules.config

@@ -252,16 +252,14 @@ process {
         ]
     }
 
-    if(!params.annotate) {
-        withName: "^.*:VCF_GENOTYPE_SV_PARAGRAPH:TABIX_FAMILY\$" {
-            publishDir = [
-                enabled: true,
-                overwrite: true,
-                path: { "${params.outdir}/ready/${meta.family}" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename ==~ /^.*.vcf.gz.tbi$/ ? filename.replace("_genotyped", "") : null }
-            ]
-        }
+    withName: "^.*:VCF_GENOTYPE_SV_PARAGRAPH:TABIX_FAMILY\$" {
+        publishDir = [
+            enabled: !params.annotate,
+            overwrite: true,
+            path: { "${params.outdir}/ready/${meta.family}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename ==~ /^.*.vcf.gz.tbi$/ ? filename.replace("_genotyped", "") : null }
+        ]
     }
 
     /*
@@ -271,8 +269,17 @@ process {
     */
 
     if(params.annotate){
-        withName: "^.*:ENSEMBLVEP_VEP\$" {
-            container = "nfcore/vep:${params.vep_version}.${params.genome}"
+
+        withName: "^.*VCF_ANNOTATE_VEP_ANNOTSV_VCFANNO:ANNOTSV_ANNOTSV\$" {
+            ext.args = "-vcf 1"
+        }
+
+        withName: "^.*VCF_ANNOTATE_VEP_ANNOTSV_VCFANNO:TABIX_ANNOTSV\$" {
+            ext.prefix = params.annotsv_file_name
+        }
+
+        withName: "^.*VCF_ANNOTATE_VEP_ANNOTSV_VCFANNO:ENSEMBLVEP_VEP\$" {
+            container = {workflow.stubRun ? "quay.io/biocontainers/ensembl-vep:108.2--pl5321h4a94de4_0" : "nfcore/vep:${params.vep_version}.${params.genome}"}
             ext.prefix = {"${meta.id}_annotated"}
             ext.args = {[
                 // specify we use VCF files
@@ -296,22 +303,19 @@ process {
                 (params.vep_structuralvariantoverlap && params.genomes1000_sv) ?    "--plugin StructuralVariantOverlap,file=${params.genomes1000_sv.split('/')[-1]}": "",
                 (params.vep_phenotypes) ?                                           "--plugin Phenotypes,file=${params.phenotypes.split('/')[-1]}": ""
             ].join(' ').trim()}
-            publishDir = [
-                enabled: true,
-                overwrite: true,
-                path: { "${params.outdir}/ready/${meta.family}" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename ==~ /^.*.vcf.gz$/ ? filename.replace("_annotated", "") : null }
-            ]
         }
 
-        withName: "^.*:TABIX_ANNOTATED\$" {
+        withName: "^.*VCF_ANNOTATE_VEP_ANNOTSV_VCFANNO:VCFANNO\$" {
+            ext.args = "-permissive-overlap"
+        }
+
+        withName: "^.*VCF_ANNOTATE_VEP_ANNOTSV_VCFANNO:TABIX_ANNOTATED\$" {
             publishDir = [
                 enabled: true,
                 overwrite: true,
                 path: { "${params.outdir}/ready/${meta.family}" },
                 mode: params.publish_dir_mode,
-                saveAs: { filename -> filename ==~ /^.*.vcf.gz.tbi$/ ? filename.replace("_annotated", "") : null }
+                saveAs: { filename -> filename != "versions.yml" ? filename : null }
             ]
         }
     }

main.nf

@@ -25,6 +25,7 @@ params.genomes1000_sv       = WorkflowMain.getGenomeAttribute(params, 'genomes10
 params.genomes1000_sv_tbi   = WorkflowMain.getGenomeAttribute(params, 'genomes1000_sv_tbi')
 params.phenotypes           = WorkflowMain.getGenomeAttribute(params, 'phenotypes')
 params.phenotypes_tbi       = WorkflowMain.getGenomeAttribute(params, 'phenotypes_tbi')
+params.annotsv_annotations  = WorkflowMain.getGenomeAttribute(params, 'annotsv_annotations')
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

modules.json

@@ -5,6 +5,17 @@
         "https://github.com/nf-core/modules.git": {
             "modules": {
                 "nf-core": {
+                    "annotsv/annotsv": {
+                        "branch": "master",
+                        "git_sha": "28708bf9ef55937d87ff6604cb36a26b3275c43f",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/annotsv/annotsv/annotsv-annotsv.diff"
+                    },
+                    "annotsv/installannotations": {
+                        "branch": "master",
+                        "git_sha": "b68aee26a00c3578710004072a10927660d16015",
+                        "installed_by": ["modules"]
+                    },
                     "bcftools/concat": {
                         "branch": "master",
                         "git_sha": "582ff1755bdd205c65e2ba4c31e0a008dae299ec",
@@ -42,7 +53,7 @@
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "b6d4d476aee074311c89d82a69c1921bd70c8180",
+                        "git_sha": "7101db4432d3268b7fcb5b8f75fa0a022dc5561b",
                         "installed_by": ["modules"]
                     },
                     "delly/call": {
@@ -53,7 +64,7 @@
                     },
                     "ensemblvep/vep": {
                         "branch": "master",
-                        "git_sha": "bea3ca998816a7f812b1bbbcb27c3a9ffbac0706",
+                        "git_sha": "ac924c4ba0be25f79248b51be0c9fbfa404b6030",
                         "installed_by": ["modules"]
                     },
                     "gridss/gridss": {
@@ -123,14 +134,24 @@
                     },
                     "tabix/bgziptabix": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "da53f7da4ff34b920bb3f186d151184bd440e3b5",
                         "installed_by": ["modules"]
                     },
                     "tabix/tabix": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
+                    "untar": {
+                        "branch": "master",
+                        "git_sha": "cc1f997fab6d8fde5dc0e6e2a310814df5b53ce7",
+                        "installed_by": ["modules"]
+                    },
+                    "vcfanno": {
+                        "branch": "master",
+                        "git_sha": "8b97329e850add26d11d822209cc6712f829e12a",
+                        "installed_by": ["modules"]
+                    },
                     "whamg": {
                         "branch": "master",
                         "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",