add process and config for vcf2maf

conf/modules.config

@@ -212,4 +212,12 @@ process {
         ]
     }
 
+    withName: 'VCF2MAF' {
+        publishDir = [
+            path: { "${params.outdir}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : "${meta.key}/vcf2maf/${filename}" },
+        ]
+    }
+
 }

conf/refdata.config

@@ -14,12 +14,14 @@ params {
     }
 
     genome {
+        build = 'GRCh38'
         fasta = 'genomes/GRCh38_umccr/GRCh38_full_analysis_set_plus_decoy_hla.fa'
         fai   = 'genomes/GRCh38_umccr/samtools_index/1.16/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai'
         dict  = 'genomes/GRCh38_umccr/samtools_index/1.16/GRCh38_full_analysis_set_plus_decoy_hla.fa.dict'
     }
 
     miscdata_paths {
+        vep_dir = "databases/pcgr/VEP/"
         pcgr_dir = "databases/pcgr/v${params.data_versions.pcgr}/"
         snpeff_dir = "databases/snpeff/v${params.data_versions.snpeff}/"
 

modules/local/vcf2maf/Dockerfile

@@ -0,0 +1,16 @@
+FROM ubuntu:24.04
+
+ARG DEBIAN_FRONTEND=noninteractive
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    bash coreutils procps findutils grep sed gawk \
+    gzip bzip2 xz-utils tar zip unzip \
+    curl wget ca-certificates git \
+    perl libjson-perl libtext-csv-perl libarchive-zip-perl \
+    libdbi-perl libdbd-sqlite3-perl \
+    bcftools samtools tabix \
+ && rm -rf /var/lib/apt/lists/*
+
+# vcf2maf scripts
+RUN git clone --depth 1 https://github.com/mskcc/vcf2maf.git /opt/vcf2maf \
+ && ln -s /opt/vcf2maf/vcf2maf.pl /usr/local/bin/vcf2maf \
+ && ln -s /opt/vcf2maf/maf2vcf.pl /usr/local/bin/maf2vcf

modules/local/vcf2maf/main.nf

@@ -0,0 +1,54 @@
+process VCF2MAF {
+    tag "${meta.id}"
+    label 'process_medium'
+
+    container 'docker.io/qclayssen/vcf2maf:debian_v1.6.22'
+
+    input:
+    tuple val(meta), path(vcf)
+    path genome_fasta
+    val genome_build
+
+
+    output:
+    tuple val(meta), path("*.maf"), emit: maf
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def uncompressed_vcf = "${meta.id}-temp.vcf"
+
+    """
+    gunzip -c ${vcf} > ${uncompressed_vcf}
+
+    vcf2maf \\
+        --inhibit-vep \\
+        --input-vcf ${uncompressed_vcf} \\
+        --output-maf ${meta.id}.maf \\
+        --ref-fasta ${genome_fasta} \\
+        --tumor-id ${meta.tumor_id} \\
+        --normal-id ${meta.normal_id} \\
+        --ncbi-build ${genome_build} \\
+        ${args}
+
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        vcf2maf: \$(vcf2maf.pl --help | grep -o 'vcf2maf [0-9.]*' | sed 's/vcf2maf //' || echo "1.6.22")
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.maf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        vcf2maf: 1.6.22
+    END_VERSIONS
+    """
+}

workflows/sash.nf

@@ -48,6 +48,7 @@ include { BOLT_SV_SOMATIC_ANNOTATE   } from '../modules/local/bolt/sv_somatic/an
 include { BOLT_SV_SOMATIC_PRIORITISE } from '../modules/local/bolt/sv_somatic/prioritise/main'
 include { ESVEE_CALL                 } from '../modules/local/esvee/call/main'
 include { PAVE_SOMATIC               } from '../modules/local/pave/somatic/main'
+include { VCF2MAF                    } from '../modules/local/vcf2maf/main'
 
 include { LINX_ANNOTATION            } from '../subworkflows/local/linx_annotation'
 include { LINX_PLOTTING              } from '../subworkflows/local/linx_plotting'
@@ -186,6 +187,35 @@ workflow SASH {
 
 
 
+    //
+    // Convert somatic VCF to MAF format
+    //
+
+    // channel: [ meta_vcf2maf, smlv_somatic_vcf ]
+    ch_vcf2maf_inputs = ch_smlv_somatic_out.map { meta, vcf -> 
+        def meta_vcf2maf = [
+            key: meta.id,
+            id: meta.id,
+            tumor_id: meta.tumor_id,
+            normal_id: meta.normal_id,
+        ]
+        return [meta_vcf2maf, vcf] 
+    }
+
+    VCF2MAF(
+        ch_vcf2maf_inputs,
+        genome.fasta,
+        genome.build
+    )
+
+    ch_versions = ch_versions.mix(VCF2MAF.out.versions)
+
+    // channel: [ meta, somatic_maf ]
+    ch_vcf2maf_out = VCF2MAF.out.maf
+
+
+
+
     //
     // Germline small variants
     //
@@ -428,7 +458,6 @@ workflow SASH {
 
 
 
-
     //
     // Generate the cancer report
     //