hiplexpipe_BRASTRAP_exome_panel_variant2table.nf

#!/usr/bin/env nextflow

// Required Inputs
refFolder      = file("/projects/vh83/reference/genomes/b37/bwa_0.7.12_index/")
inputDirectory = file('./fastqs')
tmp_dir        = file('/scratch/vh83/tmp/')

//project specific bed files

vardictBed       = file("/projects/vh83/reference/brastrap_specific/vardict/BRASTRAP_721717_8column.bed")
intervalFile     = file("/projects/vh83/reference/brastrap_specific/BRA-STRAP_621717_100.final.roverfile_g37.numsort.sorted.bed")
restrictedBed    = file("/projects/vh83/reference/brastrap_specific/BRA-STRAP_coding_regions_targeted_sort.bed")
primer_bedpe_file= file("/projects/vh83/reference/prostrap/final_prostrap_b37_bedpe_bamclipper.txt")

// Getting Reference Files
refBase          = "$refFolder/human_g1k_v37_decoy"
ref              = file("${refBase}.fasta")
refDict          = file("${refBase}.dict")
refFai           = file("${refBase}.fasta.fai")
millsIndels      = file("${refFolder}/accessory_files/Mills_and_1000G_gold_standard.indels.b37.vcf")
dbSNP            = file("${refFolder}/accessory_files/dbsnp_138.b37.vcf")
genome_file      = file("/projects/vh83/reference/genomes/b37/accessory_files/human_g1k_v37_decoy_GenomeFile.txt")
header           = file("/home/jste0021/vh83/reference/genomes/b37/vcf_contig_header_lines.txt")
af_thr           = 0.1
rheader          = file("/projects/vh83/pipelines/code/Rheader.txt")

//Annotation resources
dbsnp_b37       = file("/projects/vh83/reference/genomes/b37/accessory_files/dbsnp_138.b37.vcf")
other_vep       = file("/usr/local/vep/90/ensembl-vep/cache")
vep_brcaex      = file("/projects/vh83/reference/annotation_databases/BRCA-Exchange/BRCA-exchange_accessed-180118/BRCA-exchange_accessed-180118.sort.vcf.gz")
vep_gnomad      = file("/projects/vh83/reference/annotation_databases/gnomAD/gnomad.exomes.r2.0.2.sites/gnomad.exomes.r2.0.2.sites.vcf.gz")
vep_revel       = file("/projects/vh83/reference/annotation_databases/REVEL/REVEL-030616/revel_all_chromosomes.vcf.gz")
vep_maxentscan  = file("/projects/vh83/reference/annotation_databases/MaxEntScan/MaxEntScan_accessed-240118")
vep_exac        = file("/projects/vh83/reference/annotation_databases/ExAC/ExAC_nonTCGA.r0.3.1/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz")
vep_dbnsfp      = file("/projects/vh83/reference/annotation_databases/dbNSFP/dbNSFPv2.9.3-VEP/dbNSFP-2.9.3.gz")
vep_dbscsnv     = file("/projects/vh83/reference/annotation_databases/dbscSNV/dbscSNV1.0-VEP/dbscSNV.txt.gz")
vep_cadd        = file("/projects/vh83/reference/annotation_databases/CADD/CADD-v1.3/1000G_phase3.tsv.gz")

// Tools
picardJar      = '~/picard.jar'
bwaModule      = 'bwa/0.7.17-gcc5'
samtoolsModule = 'samtools/1.9'
bamclipper_exe = '/projects/vh83/local_software/bamclipper/bamclipper.sh'
gatkJar        = '/usr/local/gatk/3.7/bin/GenomeAnalysisTK.jar'

// Global Resource Configuration Options
globalExecutor    = 'slurm'
globalStageInMode = 'symlink'
globalCores       = 1
bwaCores	      = 4
vepCores          = 4
globalMemoryS     = '4 GB'
globalMemoryM     = '8 GB'
globalMemoryL     = '64 GB'
globalTimeS       = '10m'
globalTimeM       = '1h'
globalTimeL       = '24h'
globalQueueS      = 'short'
globalQueueL      = 'comp'

// Creating channel from input directory
ch_inputFiles = Channel.fromPath("./mpileup/*.gz").map{file -> tuple(file.name.take(file.name.lastIndexOf('_')), file)}
ch_inputIndexes = Channel.fromPath("./mpileup/*.gz.tbi").map{file -> tuple(file.name.take(file.name.lastIndexOf('_')), file)}
ch_combined = ch_inputFiles.join(ch_inputIndexes)



process CoverageBed {
    input:
        set sample, file(vcf), file(index) from ch_combined
    output:
        set sample, file("${sample}.vcftable.txt") into ch_tables
    
    publishDir path: './metrics_for_vcf', mode: 'copy'

    executor    globalExecutor
    stageInMode globalStageInMode
    cpus        1
    memory      globalMemoryS
    time        globalTimeS
    queue       globalQueueL
    module      'gatk/3.7'
    

    script:
    """
    java -Xmx4g -jar $gatkJar -T VariantsToTable -V ${vcf} -R ${ref} -F CHROM -F POS -F DP -o ${sample}.vcftable.txt
    """
}