Add VEP annotation via subworkflow

CHANGELOG.md

@@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- [#21](https://github.com/qbic-pipelines/vcftomaf/pull/21) - Add VEP annotation via subworkflow (@famosab)
+
 ### `Fixed`
 
 ### `Dependencies`

conf/modules.config

@@ -57,6 +57,7 @@ process {
             //specify to avoid publishing, overwritten otherwise
             enabled: false
         ]
+        ext.args = { '-f' }
     }
 
     withName: UNTAR {
@@ -93,4 +94,8 @@ process {
         ]
     }
 
+    withName: 'ENSEMBLVEP_VEP' {
+        ext.args = { '--vcf  --compress_output bgzip' }
+    }
+
 }

conf/test.config

@@ -29,5 +29,6 @@ params {
     intervals    = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.bed'
     genome       = 'GATK.GRCh38'
     filter       = false
+    run_vep      = true
 
 }

docs/usage.md

@@ -94,7 +94,7 @@ Chain file, if liftover should be done
 The input vcf files are PASS filtered by default.
 Additionally, if the path to a file containing the targeted intervals for panel sequencing data is specified, off-target regions will be filtered out.
 
-### `--filter``
+### `--filter`
 
 Boolean flag to enable filtering of the variants keeping only variants marked as `PASS` when set to `true`. Default is false.
 

main.nf

@@ -37,8 +37,11 @@ workflow QBICPIPELINES_VCFTOMAF {
     //
     // SET PARAMETERS
     //
-    params.fasta = getGenomeAttribute('fasta')
-    params.dict = getGenomeAttribute('dict')
+    params.fasta               = getGenomeAttribute('fasta')
+    params.dict                = getGenomeAttribute('dict')
+    params.vep_cache_version   = getGenomeAttribute('vep_cache_version')
+    params.vep_genome          = getGenomeAttribute('vep_genome')
+    params.vep_species         = getGenomeAttribute('vep_species')
 
     // Extra files
     intervals      = params.intervals      ? Channel.fromPath(params.intervals).collect()      : Channel.value([])
@@ -52,8 +55,11 @@ workflow QBICPIPELINES_VCFTOMAF {
     genome        = params.genome   ?: Channel.empty()
 
     // VEP cache
-    vep_cache          = Channel.value([]) //params.vep_cache ? Channel.fromPath(params.vep_cache).collect() : Channel.value([])
+    vep_cache          = params.vep_cache ? Channel.fromPath(params.vep_cache).collect() : Channel.value([])
     vep_cache_unpacked = Channel.value([])
+    vep_cache_version  = params.vep_cache_version
+    vep_genome         = params.vep_genome
+    vep_species        = params.vep_species
 
 
     //
@@ -68,7 +74,10 @@ workflow QBICPIPELINES_VCFTOMAF {
         liftover_chain,
         genome,
         vep_cache,
-        vep_cache_unpacked
+        vep_cache_unpacked,
+        vep_cache_version,
+        vep_genome,
+        vep_species
     )
 
     emit:

modules.json

@@ -10,6 +10,11 @@
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
+                    "ensemblvep/vep": {
+                        "branch": "master",
+                        "git_sha": "6e3585d9ad20b41adc7d271009f8cb5e191ecab4",
+                        "installed_by": ["modules", "vcf_annotate_ensemblvep"]
+                    },
                     "gunzip": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
@@ -28,7 +33,7 @@
                     "tabix/tabix": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules", "vcf_annotate_ensemblvep"]
                     },
                     "untar": {
                         "branch": "master",
@@ -59,6 +64,11 @@
                         "branch": "master",
                         "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c",
                         "installed_by": ["subworkflows"]
+                    },
+                    "vcf_annotate_ensemblvep": {
+                        "branch": "master",
+                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
+                        "installed_by": ["subworkflows"]
                     }
                 }
             }