nf-core · ramprasadn · Nov 24, 2023 · Nov 23, 2023 · Nov 23, 2023 · Nov 23, 2023
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - 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)
+- A new parameter `svdb_query_bedpedbs` to provide bedpe files as databases for SVDB query [#449](https://github.com/nf-core/raredisease/pull/449)
 
 ### `Changed`
 

diff --git a/conf/modules/annotate_structural_variants.config b/conf/modules/annotate_structural_variants.config
@@ -24,8 +24,14 @@ process {
             ]
         }
 
-        withName: '.*ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY' {
-            ext.prefix = { "${meta.id}_svdbquery" }
+        withName: '.*ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_BEDPE' {
+            ext.when  = {!params.svdb_query_bedpedbs.equals(null)}
+            ext.prefix = { "${meta.id}_bedpedb" }
+        }
+
+        withName: '.*ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_DB' {
+            ext.when  = {!params.svdb_query_dbs.equals(null)}
+            ext.prefix = { "${meta.id}_vcfdb" }
         }
 
         withName: '.*ANNOTATE_STRUCTURAL_VARIANTS:PICARD_SORTVCF' {

diff --git a/docs/usage.md b/docs/usage.md
@@ -242,15 +242,15 @@ no header and the following columns: `CHROM POS REF_ALLELE ALT_ALLELE AF`. Sampl
 
 ##### 8. SV annotation & Ranking
 
-| Mandatory                  | Optional           |
-| -------------------------- | ------------------ |
-| genome                     | reduced_penetrance |
-| svdb_query_dbs<sup>1</sup> |                    |
-| vep_cache_version          | vep_filters        |
-| vep_cache                  |                    |
-| score_config_sv            |                    |
-
-<sup>1</sup> A CSV file that describes the databases (VCFs) used by SVDB for annotating structural variants. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/svdb_querydb_files.csv). Information about the column headers can be found [here](https://github.com/J35P312/SVDB#Query).
+| Mandatory                                      | Optional           |
+| ---------------------------------------------- | ------------------ |
+| genome                                         | reduced_penetrance |
+| svdb_query_dbs/svdb_query_bedpedbs<sup>1</sup> |                    |
+| vep_cache_version                              | vep_filters        |
+| vep_cache                                      |                    |
+| score_config_sv                                |                    |
+
+<sup>1</sup> A CSV file that describes the databases (VCFs or BEDPEs) used by SVDB for annotating structural variants. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/svdb_querydb_files.csv). Information about the column headers can be found [here](https://github.com/J35P312/SVDB#Query).
 
 ##### 9. Mitochondrial annotation
 

diff --git a/modules.json b/modules.json
@@ -102,7 +102,7 @@
                     },
                     "eklipse": {
                         "branch": "master",
-                        "git_sha": "39656f68219340420f03bd54a68e111c86e107e6",
+                        "git_sha": "0031772de29283811deb989a5b42d0310d35ec22",
                         "installed_by": ["modules"]
                     },
                     "ensemblvep/filtervep": {
@@ -417,7 +417,7 @@
                     },
                     "svdb/query": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "2a35cf4643135d51284236bc2835ee8b810c971d",
                         "installed_by": ["modules"]
                     },
                     "tabix/bgzip": {

diff --git a/modules/nf-core/eklipse/environment.yml b/modules/nf-core/eklipse/environment.yml
diff --git a/modules/nf-core/eklipse/main.nf b/modules/nf-core/eklipse/main.nf
diff --git a/modules/nf-core/eklipse/meta.yml b/modules/nf-core/eklipse/meta.yml
diff --git a/modules/nf-core/eklipse/tests/main.nf.test b/modules/nf-core/eklipse/tests/main.nf.test
diff --git a/modules/nf-core/eklipse/tests/main.nf.test.snap b/modules/nf-core/eklipse/tests/main.nf.test.snap
diff --git a/modules/nf-core/eklipse/tests/tags.yml b/modules/nf-core/eklipse/tests/tags.yml
diff --git a/modules/nf-core/svdb/query/environment.yml b/modules/nf-core/svdb/query/environment.yml
diff --git a/modules/nf-core/svdb/query/main.nf b/modules/nf-core/svdb/query/main.nf
diff --git a/modules/nf-core/svdb/query/meta.yml b/modules/nf-core/svdb/query/meta.yml
diff --git a/modules/nf-core/svdb/query/tests/main.nf.test b/modules/nf-core/svdb/query/tests/main.nf.test
diff --git a/modules/nf-core/svdb/query/tests/main.nf.test.snap b/modules/nf-core/svdb/query/tests/main.nf.test.snap
diff --git a/modules/nf-core/svdb/query/tests/tags.yml b/modules/nf-core/svdb/query/tests/tags.yml
diff --git a/nextflow.config b/nextflow.config
@@ -37,6 +37,10 @@ params {
     cadd_resources             = null
     platform                   = 'illumina'
 
+    // File params
+    svdb_query_bedpedbs        = null
+    svdb_query_dbs             = null
+
     // Alignment
     aligner                    = 'bwamem2'
     rmdup                      = false

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -288,11 +288,19 @@
                     "pattern": "^\\S+\\.dict$",
                     "description": "Path to the genome dictionary file"
                 },
+                "svdb_query_bedpedbs": {
+                    "type": "string",
+                    "exists": true,
+                    "format": "file-path",
+                    "description": "Databases used for structural variant annotation in chrA-posA-chrB-posB-type-count-frequency format.",
+                    "fa_icon": "fas fa-file-csv",
+                    "help_text": "Path to comma-separated file containing information about the databases used for structural variant annotation."
+                },
                 "svdb_query_dbs": {
                     "type": "string",
                     "exists": true,
                     "format": "file-path",
-                    "description": "Databases used for structural variant annotation.",
+                    "description": "Databases used for structural variant annotation in vcf format.",
                     "fa_icon": "fas fa-file-csv",
                     "help_text": "Path to comma-separated file containing information about the databases used for structural variant annotation."
                 },