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nextflow.config
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nextflow.config
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manifest {
description = 'Somatic variant calling in tumor/normal paired or single sampels'
nextflowVersion = '> 20.07.1'
}
profiles {
hopper {
singularity {
enabled = true
runOptions = '--bind /fs1/ --bind /local/ --bind /mnt/beegfs/ --bind /fs2/'
}
env{
SENTIEON_LICENSE='10.139.0.101:8990'
bwt_max_mem='70G'
}
process {
queue = params.queue
executor = 'slurm'
withLabel: 'process_high' {
memory = 70.GB
time = 12.h
cpus = 50
}
withLabel: 'process_medium' {
memory = 32.GB
time = 12.h
cpus = 16
}
withLabel: 'process_low' {
memory = 16.GB
time = 2.h
cpus = 8
}
withLabel : 'process_single' {
memory = 40.GB
time = 5.h
cpus = 2
}
}
params {
// GENERAL PATHS //
refpath = '/fs1/resources/ref/hg38/'
outdir = '/fs1/results/'
subdir = 'tumwgs'
crondir = '/fs1/results/cron/'
gens_accessdir = "/access/wgs/plot_data"
// SENTIEON CONFIGS //
//genomic_shards_file = "$baseDir/shards_38.csv"
//genomic_shards_num = 32 , 17
genomic_shards_file = "$baseDir/shards_400MB.csv"
genomic_shards_num = 9
bwa_shards = 8
shardbwa = true
copy = true
intersect_bed = "${refpath}/bed/wgsexome/hg38_ens98_allcodingexons20bppadding_allclinvar5bppadding_agilent.noalt.bed"
// FASTA //
genome_file="${refpath}/fasta/GCA_000001405.15_GRCh38_no_alt_analysis_set_nochr.fna"
GENOMEDICT="${refpath}/fasta/GCA_000001405.15_GRCh38_no_alt_analysis_set_nochr.dict"
// VEP REFERENCES AND ANNOTATION DBS //
CADD = "${refpath}/annotation_dbs/whole_genome_SNVs.tsv.gz"
VEP_FASTA = "${refpath}/vep/.vep/homo_sapiens_merged/98_GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa.gz"
MAXENTSCAN = "${refpath}/vep/.vep/Plugins/MaxEntScan_scripts"
VEP_CACHE = "${refpath}/vep/.vep"
GNOMAD = "${refpath}/annotation_dbs/gnomad_2.1/gnomad.exomes.r2.1.sites.grch38.ALLchr.vcf.gz,gnomADg,vcf,exact,0,AF_popmax,AF,popmax"
PHYLOP = "${refpath}/annotation_dbs/hg38.phyloP100way.bw,phyloP100way,bigwig"
PHASTCONS = "${refpath}/annotation_dbs/hg38.phastCons100way.bw,phastCons,bigwig"
// ANNOTATION DBS GENERAL //
KNOWN = "${refpath}/annotation_dbs/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz"
CLINVAR = "${refpath}/annotation_dbs/clinvar38_latest.vcf.gz"
SNPEFF_DIR = "${refpath}/snpeff"
COV_INTERVAL_LIST = "${refpath}/gatk_cnv/targets_preprocessed_100bp_bins.interval_list"
GATK_PON_FEMALE = "${refpath}/gatk_cnv/20200204_female_cnvpon_100bp.hdf5"
GATK_PON_MALE = "${refpath}/gatk_cnv/20200204_male_cnvpon_100bp.hdf5"
FASTGNOMAD_REF = "${refpath}/annotation_dbs/gnomad_hg38.0.00001.dat"
GENS_GNOMAD = "${refpath}/annotation_dbs/gnomad_hg38.0.05.txt"
GATK_GNOMAD = "${refpath}/gatk_cnv/gnomad_5pct.intervals"
PON_freebayes = "${refpath}/tumwgs/PON_freebayes_206_wgs"
PON_vardict = "${refpath}/tumwgs/PON_vardict_206_wgs"
GENE_BED_PC = "${refpath}/gtf/gencode.v33.annotation.genes.proteincoding.bed"
GENE_BED_ALL = "${refpath}/gtf/gencode.v33.annotation.genes.bed"
SNV_HARD_FILTER = true
TN_MODEL = "/fs1/saile/prj/resources/tumwgs/model_sentieon/SentieonTNscopeModel_GiAB_HighAF_LowFP-201711.05.model"
panels {
'solid' {
PANEL_SNV = "${refpath}/tumwgs/snv.panel"
PANEL_CNV = "${refpath}/tumwgs/cna.panel"
PANEL_FUS = "${refpath}/tumwgs/fusion.panel"
}
'hema' {
PANEL_SNV = "${refpath}/tumwgs/snv.panel.AL"
PANEL_CNV = "${refpath}/tumwgs/cna.panel.AL"
PANEL_FUS = "${refpath}/tumwgs/fusion.panel.AL"
}
}
}
}
trannel {
singularity{
enabled = true
runOptions = '--bind /fs1/ --bind /local/'
}
env{
SENTIEON_LICENSE='10.139.0.101:8990'
bwt_max_mem='50G'
}
process {
withLabel : 'process_high' {
memory = 50.GB
time = 12.h
cpus = 30
}
withLabel : 'process_medium' {
memory = 32.GB
time = 12.h
cpus = 16
}
withLabel : 'process_low' {
memory = 32.GB
time = 2.h
cpus = 8
}
withLabel : 'process_single' {
memory = 40.GB
time = 5.h
cpus = 1
}
}
params {
// GENERAL PATHS //
refpath = '/fs1/resources/ref/hg38/'
outdir = '/fs1/results_dev/'
subdir = 'tumwgs'
crondir = '/fs1/results_dev/cron/'
// SENTIEON CONFIGS //
genomic_shards_file = "$baseDir/shards_800MB.csv"
genomic_shards_num = 5
bwa_shards = 8
copy = false
shardbwa = true
intersect_bed = "${refpath}/bed/wgsexome/hg38_ens98_allcodingexons20bppadding_allclinvar5bppadding_agilent.noalt.bed"
// FASTA //
genome_file="${refpath}/fasta/GCA_000001405.15_GRCh38_no_alt_analysis_set_nochr.fna"
GENOMEDICT="${refpath}/fasta/GCA_000001405.15_GRCh38_no_alt_analysis_set_nochr.dict"
// VEP REFERENCES AND ANNOTATION DBS //
CADD = "${refpath}/annotation_dbs/whole_genome_SNVs.tsv.gz"
VEP_FASTA = "${refpath}/vep/.vep/homo_sapiens_merged/98_GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa.gz"
MAXENTSCAN = "${refpath}/vep/.vep/Plugins/MaxEntScan_scripts"
VEP_CACHE = "${refpath}/vep/.vep"
GNOMAD = "${refpath}/annotation_dbs/gnomad_2.1/gnomad.exomes.r2.1.sites.grch38.ALLchr.vcf.gz,gnomADg,vcf,exact,0,AF_popmax,AF,popmax"
PHYLOP = "${refpath}/annotation_dbs/hg38.phyloP100way.bw,phyloP100way,bigwig"
PHASTCONS = "${refpath}/annotation_dbs/hg38.phastCons100way.bw,phastCons,bigwig"
TN_MODEL = "/fs1/saile/prj/resources/tumwgs/model_sentieon/SentieonTNscopeModel_GiAB_HighAF_LowFP-201711.05.model"
// ANNOTATION DBS GENERAL //
KNOWN = "${refpath}/annotation_dbs/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz"
CLINVAR = "${refpath}/annotation_dbs/clinvar38_latest.vcf.gz"
SNPEFF_DIR = "${refpath}/snpeff"
COV_INTERVAL_LIST = "${refpath}/gatk_cnv/targets_preprocessed_100bp_bins.interval_list"
GATK_PON_FEMALE = "${refpath}/gatk_cnv/20200204_female_cnvpon_100bp.hdf5"
GATK_PON_MALE = "${refpath}/gatk_cnv/20200204_male_cnvpon_100bp.hdf5"
FASTGNOMAD_REF = "${refpath}/annotation_dbs/gnomad_hg38.0.00001.dat"
GENS_GNOMAD = "${refpath}/annotation_dbs/gnomad_hg38.0.05.txt"
GATK_GNOMAD = "${refpath}/gatk_cnv/gnomad_5pct.intervals"
PON_freebayes = "${refpath}/tumwgs/PON_freebayes_206_wgs"
PON_vardict = "${refpath}/tumwgs/PON_vardict_206_wgs"
GENE_BED_PC = "${refpath}/gtf/gencode.v33.annotation.genes.proteincoding.bed"
GENE_BED_ALL = "${refpath}/gtf/gencode.v33.annotation.genes.bed"
SNV_HARD_FILTER = true
panels {
'solid' {
PANEL_SNV = "${refpath}/tumwgs/snv.panel"
PANEL_CNV = "${refpath}/tumwgs/cna.panel"
PANEL_FUS = "${refpath}/tumwgs/fusion.panel"
}
'hema' {
PANEL_SNV = "${refpath}/tumwgs/snv.panel.AL"
PANEL_CNV = "${refpath}/tumwgs/cna.panel.AL"
PANEL_FUS = "${refpath}/tumwgs/fusion.panel.AL"
}
}
}
}
}
trace {
overwrite = true
}