diff --git a/nextflow.config b/nextflow.config
index 0144204ccf..a688e115cd 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -15,7 +15,6 @@ params { // default value for params
   genome = 'GRCh38'
   help = false
   project = ''
-  vcflist =''
   verbose = false
   version = false
 }
diff --git a/processVCFs.nf b/processVCFs.nf
deleted file mode 100644
index 1d5e28204f..0000000000
--- a/processVCFs.nf
+++ /dev/null
@@ -1,108 +0,0 @@
-#!/usr/bin/env nextflow
-
-/*
-vim: syntax=groovy
--*- mode: groovy;-*-
-================================================================================
-=           combining and rough filtering VCF results of CAW                   =
-================================================================================
-*/
-
-if( !params.vcflist) {
-    help_message()
-    exit 1, 'Missing list of VCFs to merge'
-}
-if( !params.callName) {
-    help_message()
-    exit 1, 'Missing call name'
-}
-
-// make a channel from command-line entries
-vcfMappingChannel = makeVCFList(params.vcflist)
-
-// In this process we are adding a tag to each VCFs, so after the merge process we can see which caller called what.
-// Also applying a rough filter, leaving only records containing "PASS" in the 7th field in the VCF
-process addCallerInfo {
-    input:
-    set callerTag, file(rawVCF) from vcfMappingChannel
-    output:
-    file "tagged*vcf" into taggedVCF
-
-    script:
-    """
-    awk -f ${workflow.projectDir}/scripts/addCallerINFO.awk -v caller=${callerTag} ${rawVCF} > tagged${rawVCF}
-    """
-}
-
-// we will need tabix, bcftools and vcftools to do the job
-process compressAndIndexFilteredVCFs {
-
-    module 'htslib/1.3'
-    module 'bcftools/1.2'
-
-    input:
-    set file(vcfToCompress) from taggedVCF
-
-    output:
-    file "tagged*vcf.gz" into compressedVCF
-    file "tagged*vcf.gz.csi" into csiVCF
-
-    script:
-    """
-    bgzip ${vcfToCompress}
-    bcftools index ${vcfToCompress}.gz
-    """
-    
-}
-
-// we will need the names of the compressed VCFs in two channels: one to make links, and the other to the command line
-allVCFs = compressedVCF.reduce {a,b -> return a + " " + b}
-process mergeVCFs {
-    publishDir "mergedVariants",mode: 'copy'
-
-    module 'htslib/1.3'
-    module 'vcftools/0.1.14'
-
-    input:
-    set cVCFs from allVCFs
-
-    output:
-    file "${params.callName}_merged.vcf" into mergedVCF
-
-    script:
-    """
-    vcf-merge ${cVCFs} > ${params.callName}_merged.vcf
-    """
-}
-
-/*
-    We are running the script like
-
-    nextflow run processVCFs.nf --vcflist Manta=here/manta.vcf,MuTect1=there/mutect1.vcf    
-
-    so, have an input list like "Manta=here/manta.vcf,MuTect1=there/mutect1.vcf" and we want to have a channel like
-    [Manta, here/manta.vcf]
-    [MuTect1, there/mutect1.vcf]
-*/
-def makeVCFList(vcflist) {
-    // split the line at commas, and feed the list to a channel
-    entries = vcflist.split(",")
-    callChannel = Channel.from(entries)
-    // each entry in the channel looks like "tag=file.vcf" . Now split at the = sign, save the tag and the filename
-    vcfMappings = callChannel.map { line -> 
-                        list    = line.split("=") 
-                        tag     = list[0]
-                        vcfFile = file(list[1])
-                        [tag,vcfFile]
-                    }
-    
-    return vcfMappings
-}
-
-def help_message() { // Display help message
-    log.info "CANCER ANALYSIS WORKFLOW ~ processing VCFs "
-    log.info "  Usage:"
-    log.info "          nextflow run processVCF.nf -profile localhost --vcflist CALLER1=caller1.vcf,CALLER2=caller2.vcf[,...] --callName P12345 "
-    log.info "  Example:"
-    log.info "          nextflow run processVCF.nf -profile localhost --vcflist STRELKA=VariantCalling/Strelka/strelka/results/passed.somatic.snvs.vcf,MUTECT1=VariantCalling/MuTect1/results.vcf --callName P1234"
-}