Update vcf2maf configuration to adhere to hg38 as reference genome (qbic-pipelines#34)

* update conf to adhere to latest reference genome

* changelog

* update schema

* remove empty line

* update process shell

Author: famosab

CHANGELOG.md

@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+- [#34](https://github.com/qbic-pipelines/vcftomaf/pull/34) - Update vcf2maf configuration to adhere to hg38 as reference genome (@famosab)
 - [#35](https://github.com/qbic-pipelines/vcftomaf/pull/35) - Template update to 3.2.0 (@famosab)
 
 ### `Dependencies`

conf/modules.config

@@ -22,7 +22,7 @@ process {
         ext.args = { [ "",
             params.filter ? "-f PASS": "",
             "--output-type z"
-        ].join(" ").trim() }
+            ].join(" ").trim() }
     }
 
     withName: GUNZIP {
@@ -71,9 +71,9 @@ process {
             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 ",
+            "--retain-fmt AD,AF,DP,GQ,GT,STR",
+            "--retain-info AS_FilterStatus,AS_SB_TABLE,DP,MBQ,POPAF,STR,ANN,LOF,NMD",
+            "--retain-ann Allele,Consequence,IMPACT,SYMBOL,Gene,Feature_type,Feature,BIOTYPE,EXON,INTRON,HGVSc,HGVSp,CDNA_position,CDS_position,Protein_position,Amino_acids,Codons,Existing_variation,DISTANCE,STRAND,FLAGS,VARIANT_CLASS,SYMBOL_SOURCE,HGNC_ID,CANONICAL,MANE,MANE_SELECT,MANE_PLUS_CLINICAL,TSL,APPRIS,CCDS,ENSP,SWISSPROT,TREMBL,UNIPARC,UNIPROT_ISOFORM,GENE_PHENO,SIFT,PolyPhen,DOMAINS,miRNA,AF,AFR_AF,AMR_AF,EAS_AF,EUR_AF,SAS_AF,gnomADe_AF,gnomADe_AFR_AF,gnomADe_AMR_AF,gnomADe_ASJ_AF,gnomADe_EAS_AF,gnomADe_FIN_AF,gnomADe_MID_AF,gnomADe_NFE_AF,gnomADe_REMAINING_AF,gnomADe_SAS_AF,gnomADg_AF,gnomADg_AFR_AF,gnomADg_AMI_AF,gnomADg_AMR_AF,gnomADg_ASJ_AFIgnomADg_EAS_AF,gnomADg_FIN_AF,gnomADg_MID_AF,gnomADg_NFE_AF,gnomADg_REMAINING_AF,gnomADg_SAS_AF,gnomADg_EAS_AF_POPS,FREQS,CLIN_SIG,SOMATIC,PHENO,PUBMED,MOTIF_NAME,MOTIF_POS,HIGH_INF_POS,MOTIF_SCORE_CHANGE,TRANSCRIPTION_FACTORS",
             "--any-allele",
             "--ncbi-build ${params.genome.tokenize('.')[-1]}",
             "--species homo_sapiens"

conf/test_vep.config

@@ -25,7 +25,6 @@ params {
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
     // 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'

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
     filter                     = false
 
     // References

nextflow_schema.json

@@ -55,6 +55,14 @@
                     "type": "string",
                     "description": "For Liftover - dictionary for fasta file"
                 },
+                "run_vep": {
+                    "type": "boolean",
+                    "description": "Run annotation with VEP"
+                },
+                "vep_cache": {
+                    "type": "string",
+                    "description": "Path to tar.gz containing the VEP cache"
+                },
                 "email": {
                     "type": "string",
                     "description": "Email address for completion summary.",