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nextflow.config
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process.executor = 'slurm'
process.cache = 'lenient'
process.queue = 'silent_q'
process.shell = ['/bin/bash','-e']
executor { queueSize = 20 }
env {
NXF_EXECUTOR = "slurm"
//NXF_TEMP = "/mnt/scratch/SILENT/Act3/Processed/Individual/tmp/"
}
launchDir = "/mnt/scratch/SILENT/Act3/Processed/Workflow//Variant_catalogue_pipeline/"
ReferenceDir = "/mnt/common/SILENT/Act3/"
SingularityDir = "/mnt/common/SILENT/Act3/singularity/"
workdir = "/mnt/scratch/SILENT/Act3/Processed/Individual/"
//seem redundant - will remove after test run (now workdir is bound to Singularity instead)
//GLI = "/mnt/scratch/SILENT/Act3/Processed/Individual/Real_Data_2023/"
//GLI2 = "/mnt/scratch/SILENT/Act3/Processed/Individual/Real_Data_2023/"
params {
run = ""
batch = ""
reads = ""
sample_sheet = ""
outdir_ind = "/mnt/scratch/SILENT/Act3/Processed/Individual/"
outdir_pop = "/mnt/scratch/SILENT/Act3/Processed/Population/"
tmp_dir = "/mnt/scratch/SILENT/Act3/Processed/Individual//tmp"
//SAMPLE FILTERING: the filter list must be a tab-separated file, with a single column (id 's') with
//the IDs of the samples to be filtered
params.filter_samples = false
params.filter_list = ""
//Constants
SNV = "SNV"
STR = "STR"
MEI = "MEI"
SV = "SV"
MT = "MT"
chrM = "chrM"
params.assembly_MT = "GRCh38"
// Softwares directories
ExpansionHunter_dir = "/mnt/common/SILENT/Act3/ExpansionHunter-v5.0.0-linux_x86_64/bin/"
Melt_dir = "/mnt/common/SILENT/Act3/MELTv2.2.2"
haplocheck_path = '/mnt/common/SILENT/Act3/haplocheck/haplocheck'
path_R_libraries = '/mnt/common/SILENT/Act3/R/R_Libs_3.15/'
SINGULARITY_TMPDIR = '/tmp/'
//MT subworkflow necessary files
ref_genome_MT = "/mnt/common/SILENT/Act3/MT_references/Homo_sapiens_assembly38.chrM.fasta"
ref_genome_MT_index = "/mnt/common/SILENT/Act3/MT_references/Homo_sapiens_assembly38.chrM.fasta.fai"
ref_genome_MT_dict = "/mnt/common/SILENT/Act3/MT_references/Homo_sapiens_assembly38.chrM.dict"
ref_genome_MT_shifted = "/mnt/common/SILENT/Act3/MT_references/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta"
ref_genome_MT_shifted_index = "/mnt/common/SILENT/Act3/MT_references/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.fai"
ref_genome_MT_shifted_dict = "/mnt/common/SILENT/Act3/MT_references/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.dict"
blacklist_sites_hg38_MT = "/mnt/common/SILENT/Act3/MT_references/blacklist_sites.hg38.chrM.bed"
blacklist_sites_hg38_MT_index = "/mnt/common/SILENT/Act3/MT_references/blacklist_sites.hg38.chrM.bed.idx"
control_region_shifted_reference_interval_list = "/mnt/common/SILENT/Act3/MT_references/control_region_shifted.chrM.interval_list"
non_control_region_interval_list = "/mnt/common/SILENT/Act3/MT_references/non_control_region.chrM.interval_list"
ShiftBack_chain = "/mnt/common/SILENT/Act3/MT_references/ShiftBack.chain"
gnomad_MT_frequ = "/mnt/common/SILENT/Act3/MT_references/gnomad.genomes.v3.1.sites.chrM.reduced_annotations.tsv"
mitotip_predictions_table = '/mnt/common/SILENT/Act3/MT_references/mitotip_scores_08_27_2020.txt'
pon_predictions_table = '/mnt/common/SILENT/Act3/MT_references/pon_mt_trna_predictions_08_27_2020.txt'
artifact_prone_sites_bed = '/mnt/common/SILENT/Act3/MT_references/artifact_prone_sites.bed'
severity_table = "$launchDir/severity_table.tsv"
//A copy of the reference was done locally because Hail could not read the copy located in a common directory
GRCh38_MT_local_fasta = '/mnt/common/SILENT/Act3/MT_references/Homo_sapiens_assembly38.chrM.fasta'
GRCh38_MT_local_fai = '/mnt/common/SILENT/Act3/MT_references/Homo_sapiens_assembly38.chrM.fasta.fai'
//Annotation files
vep_cache_merged = "/mnt/common/SILENT/Act3/VEP/"
vep_cache_merged_version = "105"
dir_plugin = "/mnt/common/SILENT/Act3//VEP/Plugins/"
// Boilerplate options
help = false
}
profiles {
GRCh37 {
// params.ref = '/mnt/scratch/SILENT/Act3/Processed/Individual/data/hs37d5.fa'
// params.ref = '/mnt/scratch/SILENT/Act3/Processed/Individual/data/hs37d5.fa'
params.ref = '/mnt/common/DATABASES/REFERENCES/GRCh37/GENOME/GRCh37-lite.fa'
params.ref_index = '/mnt/common/DATABASES/REFERENCES/GRCh37/GENOME/GRCh37-lite.fa.fai'
//Constant
params.assembly = 'GRCh37'
params.Mitochondrial_chromosome = 'MT'
params.chrom = (1..22) + ['X', 'Y']
// params.chrom = '22'
//Annotation
params.CADD_1_6_whole_genome_SNVs = '/mnt/common/DATABASES/REFERENCES/GRCh37/CADD/V1.6/whole_genome_SNVs.tsv.gz'
params.CADD_1_6_whole_genome_SNVs_index = '/mnt/common/DATABASES/REFERENCES/GRCh37/CADD/V1.6/whole_genome_SNVs.tsv.gz.tbi'
params.CADD_1_6_InDels = '/mnt/common/DATABASES/REFERENCES/GRCh37/CADD/V1.6/InDels.tsv.gz'
params.CADD_1_6_InDels_index = '/mnt/common/DATABASES/REFERENCES/GRCh37/CADD/V1.6/InDels.tsv.gz.tbi'
params.spliceai_snv = '/mnt/common/DATABASES/REFERENCES/GRCh37/SPLICEAI/spliceai_scores.masked.snv.hg19.vcf.gz'
params.spliceai_snv_index = '/mnt/common/DATABASES/REFERENCES/GRCh37/SPLICEAI/spliceai_scores.masked.snv.hg19.vcf.gz.tbi'
params.spliceai_indel = '/mnt/common/DATABASES/REFERENCES/GRCh37/SPLICEAI/spliceai_scores.masked.indel.hg19.vcf.gz'
params.spliceai_indel_index = '/mnt/common/DATABASES/REFERENCES/GRCh37/SPLICEAI/spliceai_scores.masked.indel.hg19.vcf.gz.tbi'
//tsv files containing reduced information from gnomAD largest file - code to generate the tsv files available in the GitHub repo of pipeline
//This file is not necessary to obtain the vcf with variant frequencies and annotation
params.gnomad_SNV_frequ = '/mnt/common/SILENT/Act3/GRCh37/gnomad_old/*.tsv'
// If you haven't generated the above files, then you need to run the Initiatlisation.nf submodule, which requires the gnomad_SNV_vcf and gnomad_SNV_vcf_index files below
params.gnomad_SNV_vcf = '/mnt/common/DATABASES/REFERENCES/GRCh37/GNOMAD/V2.1.1/gnomad.genomes.r2.1.1.sites.vcf.gz'
params.gnomad_SNV_vcf_index = '/mnt/common/DATABASES/REFERENCES/GRCh37/GNOMAD/V2.1.1/gnomad.genomes.r2.1.1.sites.vcf.gz.tbi'
params.gnomad_SNV_frequency_outdir = '/mnt/common/SILENT/Act3/GRCh37/gnomad/'
//SV subworkflow specific files
params.cr_bed = '/mnt/common/SILENT/Act3/GRCh37/cr.bed.gz'
params.cr_bed_index = '/mnt/common/SILENT/Act3/GRCh37/cr.bed.gz.tbi'
params.genes_file = '/mnt/common/SILENT/Act3/GRCh37/hg19.genes.bed'
params.transposon_file = '/mnt/common/SILENT/Act3/GRCh37/transposons.txt'
params.variant_catalog = '/mnt/common/SILENT/Act3/ExpansionHunter-v5.0.0-linux_x86_64/variant_catalog/grch37/variant_catalog.json'
}
GRCh38 {
params.ref = '/mnt/common/DATABASES/REFERENCES/GRCh38/GENOME/GRCh38.p14/PrimaryChromOnly/GRCh38.p14_PrimaryOnly.fa'
params.ref_index = '/mnt/common/DATABASES/REFERENCES/GRCh38/GENOME/GRCh38.p14/PrimaryChromOnly/GRCh38.p14_PrimaryOnly.fa.fai'
//Constant
params.assembly = 'GRCh38'
params.Mitochondrial_chromosome = 'MT'
//Using with 'chr' prefix for GRCh38 - used in Hail_sample_QC.nf/.py and Hail_variant_QC.nf/py - needed for properly
//working with hail and filtering rows in hail tables for each chromosome
params.chrom = ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY']
//params.chrom = ['1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '20', '21', '22', 'X', 'Y']
// params.chrom = 'chr22'
//Annotation
params.CADD_1_6_whole_genome_SNVs = '/mnt/common/DATABASES/REFERENCES/GRCh38/CADD/V1.6/whole_genome_SNVs.tsv.gz'
params.CADD_1_6_whole_genome_SNVs_index = '/mnt/common/DATABASES/REFERENCES/GRCh38/CADD/V1.6/whole_genome_SNVs.tsv.gz.tbi'
params.CADD_1_6_InDels = '/mnt/common/DATABASES/REFERENCES/GRCh38/CADD/V1.6/gnomad.genomes.r3.0.indel.tsv.gz'
params.CADD_1_6_InDels_index = '/mnt/common/DATABASES/REFERENCES/GRCh38/CADD/V1.6/gnomad.genomes.r3.0.indel.tsv.gz.tbi'
params.spliceai_snv = '/mnt/common/DATABASES/REFERENCES/GRCh38/SPLICEAI/spliceai_scores.masked.snv.hg38.vcf.gz'
params.spliceai_snv_index = '/mnt/common/DATABASES/REFERENCES/GRCh38/SPLICEAI/spliceai_scores.masked.snv.hg38.vcf.gz.tbi'
params.spliceai_indel = '/mnt/common/DATABASES/REFERENCES/GRCh38/SPLICEAI/spliceai_scores.masked.indel.hg38.vcf.gz'
params.spliceai_indel_index = '/mnt/common/DATABASES/REFERENCES/GRCh38/SPLICEAI/spliceai_scores.masked.indel.hg38.vcf.gz.tbi'
//tsv files containing reduced information from gnomAD largest file - code to generate the tsv files available in the GitHub repo of pipeline
//This file is not necessary to obtain the vcf with variant frequencies and annotation
params.gnomad_SNV_frequ = '/mnt/common/SILENT/Act3/GRCh38/gnomad_v4.1_joint/tables/*.tsv'
// If you haven't generated the above files, then you need to run the Initiatlisation.nf submodule, which requires the gnomad_SNV_vcf and gnomad_SNV_vcf_index files below
params.gnomad_SNV_vcf = '/mnt/common/DATABASES/REFERENCES/GRCh38/GNOMAD/V3/gnomad.genomes.r3.0.sites.vcf.gz'
params.gnomad_SNV_vcf_index = '/mnt/common/DATABASES/REFERENCES/GRCh38/GNOMAD/V3/gnomad.genomes.r3.0.sites.vcf.gz.tbi'
params.gnomad_SNV_frequency_outdir = '/mnt/common/SILENT/Act3/GRCh38/gnomad/'
//SV subworkflow specific files
params.cr_bed = '/mnt/common/SILENT/Act3/GRCh38/cr_withoutchr.bed.gz'
params.cr_bed_index = '/mnt/common/SILENT/Act3//GRCh38/cr_withoutchr.bed.gz.tbi'
params.genes_file = '/mnt/common/SILENT/Act3//GRCh38/Hg38.genes.bed'
params.transposon_file = '/mnt/common/SILENT/Act3//GRCh38/transposons.txt'
params.variant_catalog ="/mnt/common/SILENT/Act3/ExpansionHunter-v5.0.0-linux_x86_64/variant_catalog/grch38/variant_catalog.json"
}
test {
params.ref = '/mnt/scratch/SILENT/Act3/Processed/Individual/data/reduced.fa'
params.ref_index = '/mnt/scratch/SILENT/Act3/Processed/Individual/data/reduced.fa.fai'
//Constant
params.assembly = 'GRCh38'
params.Mitochondrial_chromosome = 'MT'
params.chrom = ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY']
// params.chrom = 'chr22'
//Annotation
params.CADD_1_6_whole_genome_SNVs = '/mnt/common/SILENT/Act3/GRCh38/CADD/V1.6/whole_genome_SNVs.tsv.gz'
params.CADD_1_6_whole_genome_SNVs_index = '/mnt/common/SILENT/Act3/GRCh38/CADD/V1.6/whole_genome_SNVs.tsv.gz.tbi'
params.CADD_1_6_InDels = '/mnt/common/SILENT/Act3/GRCh38/CADD/V1.6/gnomad.genomes.r3.0.indel.tsv.gz'
params.CADD_1_6_InDels_index = '/mnt/common/SILENT/Act3/GRCh38/CADD/V1.6/gnomad.genomes.r3.0.indel.tsv.gz.tbi'
params.spliceai_snv = '/mnt/common/SILENT/Act3/GRCh38/SPLICEAI/spliceai_scores.masked.snv.hg38.vcf.gz'
params.spliceai_snv_index = '/mnt/common/SILENT/Act3/GRCh38/SPLICEAI/spliceai_scores.masked.snv.hg38.vcf.gz.tbi'
params.spliceai_indel = '/mnt/common/SILENT/Act3/GRCh38/SPLICEAI/spliceai_scores.masked.indel.hg38.vcf.gz'
params.spliceai_indel_index = '/mnt/common/SILENT/Act3/GRCh38/SPLICEAI/spliceai_scores.masked.indel.hg38.vcf.gz.tbi'
//tsv files containing reduced information from gnomAD largest file - code to generate the tsv files available in the GitHub repo of pipeline
//This file is not necessary to obtain the vcf with variant frequencies and annotation
params.gnomad_SNV_frequ = '/mnt/common/SILENT/Act3/GRCh38/gnomad/*.tsv'
//SV subworkflow specific files
params.cr_bed = '/mnt/scratch/SILENT/Act3/Processed/Individual/data/cr.bed.gz'
params.cr_bed_index = '/mnt/scratch/SILENT/Act3/Processed/Individual/data/cr.bed.gz.tbi'
params.genes_file = '/mnt/common/SILENT/Act3//GRCh38/Hg38.genes.bed'
params.transposon_file = '/mnt/common/SILENT/Act3//GRCh38/transposons.txt'
params.variant_catalog ="$ReferenceDir/ExpansionHunter/ExpansionHunter-v5.0.0-linux_x86_64/variant_catalog/grch38/variant_catalog.json"
}
}
// GLNexus requires access to files in workdir (the sample vcf files)
singularity {
enabled = true
autoMounts = true
runOptions = "-e -B $launchDir -B $ReferenceDir -B $SingularityDir -B $workdir"
cacheDir = "/mnt/scratch/SILENT/Act3/Processed/Individual/tmp"
}
process {
//conda
withLabel: 'conda_annotate' {
conda = "/mnt/common/WASSERMAN_SOFTWARE/AnnotateVariants/opt/AnnotateVariantsEnvironment"
memory = 32.GB
cpus = 8
}
withName: 'Hail_STR|Hail_MEI_QC|Hail_sample_QC|Hail_SV_QC|Hail_variant_MT_QC|Hail_variant_QC' {
conda = "/mnt/common/SILENT/Act3/conda/miniconda3/envs/hail"
memory = "340.GB"
cpus = "40"
}
// 4GB, 2cpus
withName: 'align_to_MT|MT_MergeVcfs|list_vcfs_txt|MEI_data_organization' {
memory = 4.GB
cpus = 2
}
// 12Gb, 8 cpus
withName: 'align_sort_output_bam|expansion_hunter|Hail_sample_QC' {
memory = 45.GB
cpus = 8
}
// 4GB, 8cpus
withName: 'STR_data_organization' {
memory = 4.GB
cpus = 8
}
withName: 'bwa_index|bcf_to_vcf' {
memory = 40.GB
cpus = 8
}
// 8GB, 4cpusi, R
withName: 'shift_back|MT_Step3_metadata_sample' {
memory = 8.GB
memory = 20.GB
cpus = 8
}
// 40GB, 8 cpus//FastQC, 2GB, 4CPUs
withName: 'fastqc' {
memory = 2.GB
cpus = 4
container = "file:///mnt/common/SILENT/Act3/singularity/fastqc.0.11.sif"
//container = "https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0"
}
//MultiQC 4GB
withName: 'bwa_index|bcf_to_vcf' {
memory = 40.GB
cpus = 8
}
// 8GB, 4cpusi, R
withName: 'shift_back|MT_Step3_metadata_sample' {
memory = 8.GB
cpus = 4
container = 'file:///mnt/common/SILENT/Act3/R/rstudio-bioconductor-Release_3_15.simg'
}
//MultiQC 4GB
withName: 'multiqc_indiv' {
memory=4.GB
container = "file:///mnt/common/SILENT/Act3/singularity/multiqc-1.9.sif"
}
//Mosdepth, 4GB
withName: 'Mosdepth' {
memory = 4.GB
container = "file:///mnt/common/SILENT/Act3/singularity/mosdepth-0.3.2.sif"
}
//DeepVariant
withName: 'deepvariant_call' {
memory = 60.GB
cpus = 39
container = "file:///mnt/common/SILENT/Act3/singularity/deepvariant-1.2.0.sif"
}
//GLnexus
withName: 'GLnexus_cli' {
memory = 200.GB
cpus = 39
container = "file:///mnt/common/SILENT/Act3/singularity/glnexus-1.4.1.sif"
}
//GATK 4GB
withName: 'MarkDuplicates|MT_MergeVcfs|MT_call_variants|Extract_MT_Read|MT_Filter_Mutect_Calls|MT_FilterOut_sites|MT_LeftAlignAndTrimVariants|MT_Liftover|MT_Merge_stat_file|MT_SamtoFastq|gnomad_frequency_table' {
memory=4.GB
container = "file:///mnt/common/SILENT/Act3/singularity/gatk4-4.2.0.sif"
}
//GATK, 4 CPUs , 8Gb
withName: 'Picard_CollectWgsMetrics|Picard_CollectWgsMetrics_MT' {
cpus = 4
memory=8.GB
container = "file:///mnt/common/SILENT/Act3/singularity/gatk4-4.2.0.sif"
}
//GATK, 4 CPUs , 2Gb
withName: 'Picard_CollectAlignmentSummaryMetrics' {
cpus = 4
memory=2.GB
container = "file:///mnt/common/SILENT/Act3/singularity/gatk4-4.2.0.sif"
}
// Picard_R, 2Gb, 4 CPUs
withName: 'Picard_QualityScoreDistribution' {
cpus=4
memory=2.GB
container = "file:///mnt/common/SILENT/Act3/singularity/picard_r.sif"
}
// Smoove, 8Gb, 3 cpus
withName: 'SV_smoove' {
cpus = 2
memory = 4.GB
container = "file:///mnt/common/SILENT/Act3/singularity/smoove_latest.sif"
}
// Manta, 6Gb, 24cpus
withName: 'SV_manta' {
cpus = 20
memory = 4.GB
container = "file:///mnt/common/SILENT/Act3/singularity/illumina_manta.sif"
}
// Concat by sample, 6Gb, 2cpus
withName: 'SV_concat_by_sample' {
memory = 6.GB
cpus = 2
container = "file:///mnt/common/SILENT/Act3/singularity/sv-dep.sif"
}
// paragraph_duphold
withName: 'SV_paragraph_duphold' {
container = "file:///mnt/common/SILENT/Act3/singularity/brentp-rare-disease-sv-v0.1.2.img"
cpus = 12
memory = 8.GB
}
//Jasmine
withName: 'SV_jasmine' {
container = "file:///mnt/common/SILENT/Act3/singularity/sv-dep.sif"
cpus = 4
memory = 6.GB
}
}