From 1ab53dcd9fe93e43d246701fb6b50d5af4d1db61 Mon Sep 17 00:00:00 2001
From: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
Date: Tue, 12 Mar 2024 19:29:13 +0000
Subject: [PATCH] remove VEP

---
 .github/workflows/ci.yml |  2 +-
 conf/modules.config      |  3 ++-
 main.nf                  |  2 +-
 nextflow.config          |  4 ++--
 nextflow_schema.json     | 14 --------------
 workflows/vcftomaf.nf    | 25 +++++++++++++------------
 6 files changed, 19 insertions(+), 31 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 3e1cd8e..6ca69e0 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -28,7 +28,7 @@ jobs:
           - "latest-everything"
         profile:
           - "test"
-          - "test_vep"
+          # - "test_vep"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
diff --git a/conf/modules.config b/conf/modules.config
index 0c3a152..1e29ca8 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -65,7 +65,8 @@ process {
 
     withName: VCF2MAF {
         ext.args = { [ "",
-            params.run_vep ? "" : "--inhibit-vep",
+            //params.run_vep ? "" : "--inhibit-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",
diff --git a/main.nf b/main.nf
index 25b5e16..c667c92 100644
--- a/main.nf
+++ b/main.nf
@@ -42,7 +42,7 @@ dict         = params.dict      ? Channel.fromPath(params.dict).collect()
 genome        = params.genome   ?: Channel.empty()
 
 // VEP cache
-vep_cache          = params.vep_cache ? Channel.fromPath(params.vep_cache).collect() : Channel.value([])
+vep_cache          = Channel.value([]) //params.vep_cache ? Channel.fromPath(params.vep_cache).collect() : Channel.value([])
 vep_cache_unpacked = Channel.value([])
 
 
diff --git a/nextflow.config b/nextflow.config
index 98d4e5d..32a1142 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -13,8 +13,8 @@ params {
     liftover_chain             = null
     input                      = null
     intervals                  = null
-    vep_cache                  = null
-    run_vep                    = false
+    //vep_cache                  = null
+    //run_vep                    = false
 
     // References
     genome                     = null
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 65d5e6b..e7b93fd 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -47,20 +47,6 @@
                     "help_text": "You will need to create a provide file with information about the targeted intervals.",
                     "fa_icon": "fas fa-file"
                 },
-                "run_vep": {
-                    "type": "boolean",
-                    "description": "Set to true to run with vep cache, set to false to inhibit running vep.",
-                    "help_text": "Specify if vep cache shall be used."
-                },
-                "vep_cache": {
-                    "type": "string",
-                    "format": "file-path",
-                    "exists": true,
-                    "pattern": "^\\S+\\.tar.gz$",
-                    "description": "Path to VEP cache.",
-                    "help_text": "Provide path to VEP cache if vcf files are not annotated with VEP.",
-                    "fa_icon": "fas fa-file"
-                },
                 "email": {
                     "type": "string",
                     "description": "Email address for completion summary.",
diff --git a/workflows/vcftomaf.nf b/workflows/vcftomaf.nf
index f73bd6b..16c930a 100644
--- a/workflows/vcftomaf.nf
+++ b/workflows/vcftomaf.nf
@@ -47,18 +47,19 @@ workflow VCFTOMAF {
     // SUBWORKFLOW: Read in samplesheet, validate and stage input files
     //
 
-    if (params.vep_cache){
-        ch_vep_cache = vep_cache.map{
-            it -> def new_id = ""
-                if(it) {
-                    new_id = it[0].simpleName.toString()
-                }
-            [[id:new_id], it]
-        }
-        // UNTAR if available
-        vep_cache_unpacked  = UNTAR(ch_vep_cache).untar.map { it[1] }
-        ch_versions         = ch_versions.mix(UNTAR.out.versions)
-    }
+    // VEP annotation is currently not supported from within vcf2maf : https://github.com/mskcc/vcf2maf/issues/335
+    // if (params.vep_cache){
+    //     ch_vep_cache = vep_cache.map{
+    //         it -> def new_id = ""
+    //             if(it) {
+    //                 new_id = it[0].simpleName.toString()
+    //             }
+    //         [[id:new_id], it]
+    //     }
+    //     // UNTAR if available
+    //     vep_cache_unpacked  = UNTAR(ch_vep_cache).untar.map { it[1] }
+    //     ch_versions         = ch_versions.mix(UNTAR.out.versions)
+    // }
 
     // BRANCH CHANNEL
     ch_samplesheet.branch{