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nextflow.config
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params {
genome = "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/bwamem2/Homo_sapiens_assembly38.fasta" // file(params.genome)
genomedict= "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/genome/Homo_sapiens_assembly38.dict"
wgsregion = "/data/nousomedr/annotation/resources_broad_hg38_v0_wgs_calling_regions.hg38.interval_list" //
millsindel = "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/GATK_resource_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz" //Mills_and_1000G_gold_standard.indels.hg38.vcf.gz"
shapeitindel = "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/GATK_resource_bundle/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz" //ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz" //file(params.gold_indels2) //
dbsnp = "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/GATK_resource_bundle/dbsnp_138.hg38.vcf.gz"
dbsnp_indel = "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/GATK_resource_bundle/dbsnp_indel.vcf"
gnomad = '/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/GNOMAD/somatic-hg38-af-only-gnomad.hg38.vcf.gz' // /data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/GNOMAD/somatic-hg38-af-only-gnomad.hg38.vcf.gz
//pon="/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/PON/hg38.noCOSMIC_ClinVar.pon.vcf.gz" //file{params.pon}
pon = "/data/nousomedr/wgs/updatedpon.vcf.gz"
kgp = "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/GATK_resource_bundle/1000G_phase1.snps.high_confidence.hg38.vcf.gz"
KRAKENBACDB = "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/kraken/20180907_standard_kraken2"
fastq_screen_conf= "${projectDir}/workflow/resources/fastq_screen.conf"
get_flowcell_lanes="${projectDir}/workflow/scripts/flowcell_lane.py"
intervals="${projectDir}/workflow/resources/hg38_v0_wgs_calling_regions.hg38.bed"
splitbed="${projectDir}/workflow/resources/split_Bed_into_equal_regions.py"
split_regions = "24" //Number of regions to split by
snpeff_genome = "GRCh38.86"
snpeff_config = "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/snpEff/4.3t/snpEff.config"
snpeff_bundle = "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/snpEff/4.3t/"
sites_vcf= "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/somalier/sites.hg38.vcf.gz"
somalier_ancestrydb="/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/somalier/1kg-somalier"
script_genderPrediction = "${projectDir}/workflow/scripts/RScripts/predictGender.R"
script_combineSamples = "${projectDir}/workflow/scripts/RScripts/combineAllSampleCompareResults.R"
script_ancestry = "${projectDir}/workflow/scripts/RScripts/sampleCompareAncestoryPlots.R"
bwagenome= "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/genome/Homo_sapiens_assembly38.fasta"
vep_cache = "/fdb/VEP/102/cache"
//Biowulf
config_profile_description = 'Biowulf nf-core config'
config_profile_contact = '[email protected]'
max_memory = 224.GB
max_cpus = 32
output = "output"
//SUB WORKFLOWS to SPLIT
PIPE_ALIGN=null
PIPE_GERMLINE=null
PIPE_VC=null
PIPE_SV=null
PIPE_QC=null
PIPE_BAMVC=null
PIPE_TONLY_ALIGN=null
PIPE_TONLY_VC=null
PIPE_BAMVC_TONLY=null
PIPE_TONLY_BAMVC=null
PIPE_TONLY_QC=null
//Set all Inputs to null
sample_sheet=null
fastq_input=null
bam_input=null
file_input=null
}
profiles {
local {
process {
executor = 'local'
withName:fc_lane {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
}
withName:fastq_screen {
container= 'docker://nciccbr/ccbr_fastq_screen_0.13.0:v2.0'
}
withName:kraken {
container= 'docker://nciccbr/ccbr_kraken_v2.1.1:v0.0.1'
}
withName:fastqc {
container= 'docker://nciccbr/ccbr_fastqc_0.11.9:v1.1'
}
withName: qualimap_bamqc {
container= 'docker://nciccbr/ccbr_qualimap:v0.0.1'
}
withName: 'samtools_flagstats|vcftools|bcftools_stats|gatk_varianteval|snpeff|somalier_extract|somalier_analysis' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
}
withName: 'multiqc' {
container= 'docker://nciccbr/ccbr_multiqc_1.9:v0.0.1'
}
withName: 'collectvariantcallmetrics' {
container= 'docker://nciccbr/ccbr_picard:v0.0.1'
}
withName: 'fastp|bwamem2|indelrealign|bqsr|gatherbqsr|samtoolsindex|applybqsr' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
}
withName:'mutect2|mutect2_t|mutect2_t_tonly|mutect2filter|mutect2filter_tonly|learnreadorientationmodel|learnreadorientationmodel_tonly|contamination_paired|contamination_tumoronly|pileup_paired_t|pileup_paired_n|pileup_paired_tonly' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
}
withName: 'strelka_tn|vardict_tn|vardict_tonly|varscan_tn|varscan_tonly|combineVariants|combineVariants_strelka' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
}
withName: 'annotvep_tn|annotvep_tonly' {
container= 'docker://dnousome/ccbr_vcf2maf:v102.0.0'
}
withName: 'svaba_somatic' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
}
}
singularity {
enabled = true
autoMounts = true
cacheDir = "$PWD/singularity"
envWhitelist='https_proxy,http_proxy,ftp_proxy,DISPLAY,SLURM_JOBID'
runOptions = '-B /data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/,/data/nousomedr/,/data/CCBR/projects/,/vf/users/,/gpfs/,/fdb'
}
}
localstub {
process {
executor = 'local'
singularity {
enabled = false
}
}
}
biowulf {
process {
executor = 'slurm'
queue = 'norm'
queueSize = 200
errorStrategy = 'finish'
maxRetries = 0
pollInterval = '2 min'
queueStatInterval = '5 min'
submitRateLimit = '6/1min'
//Default options for Slurm Nodes
cpus= '4'
time= 48.h
memory=64.GB
timeline.enabled = true
report.enabled = true
//scratch = '/lscratch/$SLURM_JOBID'
//Each Process and Container if it exists or use module in each process
withName:fastq_screen{
container= 'docker://nciccbr/ccbr_fastq_screen_0.13.0:v2.0'
memory=32.GB
time=48.h
cpus=4
}
withName:fastqc {
container= 'docker://nciccbr/ccbr_fastqc_0.11.9:v1.1'
memory=24.GB
time=24.h
cpus=8
}
withName:fastp {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
memory=24.GB
time=24.h
cpus=4
}
withName:fc_lane {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
}
withName:bwamem2 {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
memory=200.GB
time=48.h
cpus=17
}
withName:indelrealign{
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
memory=48.GB
time=72.h
cpus=16
}
withName:bqsr{
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
memory= 32.GB
time= 48.h
}
withName:gatherbqsr{
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
memory= 16.GB
time= 2.h
}
withName:applybqsr{
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
memory= 48.GB
time= 48.h
}
withName:samtoolsindex{
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
memory= 16.GB
time= 12.h
cpus= 4
}
withName: 'mutect2|mutect2_t|mutect2_t_tonly' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
memory= 48.GB
cpus= 4
time= 72.h
}
withName: 'vardict_tn|vardict_tonly|varscan_tn|varscan_tonly|combineVariants|combineVariants_strelka' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
memory= 32.GB
cpus= 2
time= 72.h
}
withName: 'strelka_tn' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
memory= 48.GB
cpus= 16
time= 72.h
}
withName:'mutect2filter|mutect2filter_tonly' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
memory= 24.GB
time= 24.h
cpus= 4
}
withName:'contamination_paired|contamination_tumoronly'{
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
memory= 24.GB
time= 24.h
}
withName:'learnreadorientationmodel|learnreadorientationmodel_tonly' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
memory= 48.GB
time= 24.h
}
withName:'mergemut2stats|mergemut2stats_tonly' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
memory= 16.GB
time= 24.h
}
withName:'pileup_paired_t|pileup_paired_n|pileup_paired_tonly' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
memory= 16.GB
time= 12.h
}
withName:'annotvep_tn|annotvep_tonly'{
container= 'docker://dnousome/ccbr_vcf2maf:v102.0.0'
memory= 32.GB
time= 24.h
cpus=16
}
withName:kraken {
container= 'docker://nciccbr/ccbr_kraken_v2.1.1:v0.0.1'
memory= 64.GB
time= 24.h
cpus=16
clusterOptions="--gres=lscratch:256"
}
withName:'deepvariant_step1' {
memory= 64.GB
time= 24.h
cpus=2
}
withName:'deepvariant_step3' {
memory= 64.GB
time= 24.h
cpus=2
clusterOptions="--gres=lscratch:256"
}
withName:'deepvariant_step2|deepvariant_combined' {
memory= 70.GB
time= 24.h
cpus= 17
queue = 'gpu'
clusterOptions="--partition=gpu --gres=gpu:v100x:1,lscratch:256"
}
withName:'somalier_extract|somalier_analysis' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
memory= 16.GB
time= 12.h
}
withName:'gatk_varianteval' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
memory= 16.GB
time= 12.h
}
withName:'qualimap_bamqc' {
container= 'docker://nciccbr/ccbr_qualimap:v0.0.1'
cpus= 8
memory= 120.GB
time= 48.h
//errorStrategy = { task.exitStatus in [1,143,137,104,134,139] ? 'retry' : task.exitStatus in [143, 255] ? 'ignore' : 'finish' }
}
withName:'cobalt|amber|purple' {
memory= 64.GB
time= 12.h
cpus=16
}
withName:'svaba_somatic' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
memory= 64.GB
time= 24.h
cpus=16
}
}
//Container options
singularity {
enabled = true
autoMounts = true
cacheDir = "$PWD/singularity"
envWhitelist='https_proxy,http_proxy,ftp_proxy,DISPLAY,SLURM_JOBID'
runOptions = '-B /gs10,/gs11,/gs12,/gs8,/gs9,/spin1,/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/,/data/nousomedr/,/data/CCBR/projects/,/vf/users,/gpfs,/fdb'
}
}
}