Enable VEP annotation with vcf2maf module

.github/workflows/ci.yml

@@ -35,6 +35,7 @@ jobs:
           - "singularity"
         test_name:
           - "test"
+          - "test_vep"
         isMaster:
           - ${{ github.base_ref == 'master' }}
         # Exclude conda and singularity on dev

.gitignore

@@ -7,3 +7,6 @@ testing/
 testing*
 *.pyc
 null/
+nf-*
+.vscode/*
+.vscode

conf/modules.config

@@ -68,14 +68,15 @@ process {
 
     withName: VCF2MAF {
         ext.args = { [ "",
-            //params.run_vep ? "" : "--inhibit-vep",
-            "--inhibit-vep",
+            params.run_vep ? "" : "--inhibit-vep",
             meta.normal_id ? "--normal-id ${meta.normal_id} --vcf-normal-id ${meta.vcf_normal_id}" : "",
             meta.tumor_id  ? "--tumor-id ${meta.tumor_id} --vcf-tumor-id ${meta.vcf_tumor_id}"     : "",
             "--retain-info HGVSp_VEP,HGVSc_VEP,genename,codonpos,clinvar_hgvs,cds_strand,aaref,aaalt,aapos,VEP_canonical,MutPred_AAchange",
             "--retain-ann HGVSp_VEP,HGVSc_VEP,genename,codonpos,clinvar_hgvs,cds_strand,aaref,aaalt,aapos,VEP_canonical,MutPred_AAchange",
             "--retain-fmt HGVSp_VEP,HGVSc_VEP,genename,codonpos,clinvar_hgvs,cds_strand,aaref,aaalt,aapos,VEP_canonical,MutPred_AAchange ",
-            "--any-allele"
+            "--any-allele",
+            "--ncbi-build ${params.genome.tokenize('.')[-1]}",
+            "--species homo_sapiens"
         ].join(" ").trim() }
         publishDir = [
             path: { "${params.outdir}/maf" },

conf/test_vep.config

@@ -10,23 +10,27 @@
 ----------------------------------------------------------------------------------------
 */
 
+process {
+    // Limit resources so that this can run on GitHub Actions
+    resourceLimits = [
+        cpus: 2,
+        memory: '6.GB',
+        time: '6.h'
+    ]
+}
+
+
 params {
     config_profile_name        = 'Test VEP profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
-
     // Input data
 
     input        = "${projectDir}/tests/samplesheets/samplesheet.csv"
     fasta        = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
     intervals    = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.bed'
-    vep_cache    = 'https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/genome/vep.tar.gz'
+    vep_cache    = 'https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/genome/vep_cache_113.tar.gz'
     genome       = 'GATK.GRCh38'
     run_vep      = true
 
-
 }

docs/usage.md

@@ -98,13 +98,13 @@ Additionally, if the path to a file containing the targeted intervals for panel
 
 Boolean flag to enable filtering of the variants keeping only variants marked as `PASS` when set to `true`. Default is false.
 
-<!-- ### `--vep_cache`
+### `--vep_cache`
 
 Please provide a path to a compressed vep-cache file if you wish to run vep.
 
 ### `--run_vep`
 
-Set to true if you wish to run vep. Default is false. -->
+Set to true if you wish to run vep. Default is false.
 
 ### Params file
 

main.nf

@@ -52,7 +52,7 @@ 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([])
 
 

modules.json

@@ -32,12 +32,12 @@
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "3e548877f25a5980a177cc4f81d2d2e8c24164ef",
                         "installed_by": ["modules"]
                     },
                     "vcf2maf": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "538cbd31deef6e6abe0daafa704a918ad6974699",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/vcf2maf/vcf2maf.diff"
                     }