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genomes.config
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genomes.config
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/*
* -------------------------------------------------
* Nextflow config file for reference genome
* -------------------------------------------------
* Defines reference genomes, without using iGenome paths
* Can be used by any config that customises the base
* path using $params.genomes_base / --genomes_base
*/
params {
genomes {
'GRCh37' {
ac_loci = "${params.genomes_base}/1000G_phase3_20130502_SNP_maf0.3.loci"
ac_loci_gc = "${params.genomes_base}/1000G_phase3_20130502_SNP_maf0.3.loci.gc"
bwa = "${params.genomes_base}/human_g1k_v37_decoy.fasta.{amb,ann,bwt,pac,sa}"
chr_dir = "${params.genomes_base}/Chromosomes"
chr_length = "${params.genomes_base}/human_g1k_v37_decoy.len"
dbsnp = "${params.genomes_base}/dbsnp_138.b37.vcf"
dbsnp_index = "${params.genomes_base}/dbsnp_138.b37.vcf.idx"
dict = "${params.genomes_base}/human_g1k_v37_decoy.dict"
fasta = "${params.genomes_base}/human_g1k_v37_decoy.fasta"
fasta_fai = "${params.genomes_base}/human_g1k_v37_decoy.fasta.fai"
germline_resource = "${params.genomes_base}/gnomAD.r2.1.1.GRCh37.PASS.AC.AF.only.vcf.gz"
germline_resource_index = "${params.genomes_base}/gnomAD.r2.1.1.GRCh37.PASS.AC.AF.only.vcf.gz.tbi"
intervals = "${params.genomes_base}/wgs_calling_regions_Sarek.list"
known_indels = "${params.genomes_base}/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf"
known_indels_index = "${params.genomes_base}/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.idx"
mappability = "${params.genomes_base}/out100m2_hg19.gem"
snpeff_db = 'GRCh37.75'
species = 'homo_sapiens'
vep_cache_version = '99'
}
'GRCh38' {
ac_loci = "${params.genomes_base}/1000G_phase3_GRCh38_maf0.3.loci"
ac_loci_gc = "${params.genomes_base}/1000G_phase3_GRCh38_maf0.3.loci.gc"
bwa = "${params.genomes_base}/Homo_sapiens_assembly38.fasta.64.{alt,amb,ann,bwt,pac,sa}"
chr_dir = "${params.genomes_base}/Chromosomes"
chr_length = "${params.genomes_base}/Homo_sapiens_assembly38.len"
dbsnp = "${params.genomes_base}/dbsnp_146.hg38.vcf.gz"
dbsnp_index = "${params.genomes_base}/dbsnp_146.hg38.vcf.gz.tbi"
dict = "${params.genomes_base}/Homo_sapiens_assembly38.dict"
fasta = "${params.genomes_base}/Homo_sapiens_assembly38.fasta"
fasta_fai = "${params.genomes_base}/Homo_sapiens_assembly38.fasta.fai"
germline_resource = "${params.genomes_base}/gnomAD.r2.1.1.GRCh38.PASS.AC.AF.only.vcf.gz"
germline_resource_index = "${params.genomes_base}/gnomAD.r2.1.1.GRCh38.PASS.AC.AF.only.vcf.gz.tbi"
intervals = "${params.genomes_base}/wgs_calling_regions.hg38.bed"
known_indels = "${params.genomes_base}/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz"
known_indels_index = "${params.genomes_base}/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi"
mappability = "${params.genomes_base}/out100m2_hg38.gem"
snpeff_db = 'GRCh38.86'
species = 'homo_sapiens'
vep_cache_version = '99'
}
'minimalGRCh37' {
fasta = "${params.genomes_base}/human_g1k_v37_decoy.small.fasta"
}
'smallGRCh37' {
dbsnp = "${params.genomes_base}/dbsnp_138.b37.small.vcf.gz"
fasta = "${params.genomes_base}/human_g1k_v37_decoy.small.fasta"
germline_resource = "${params.genomes_base}/gnomAD.r2.1.1.GRCh37.small.PASS.AC.AF.only.vcf.gz"
intervals = "${params.genomes_base}/small.intervals"
known_indels = "${params.genomes_base}/Mills_1000G_gold_standard_and_1000G_phase1.indels.b37.small.vcf.gz"
snpeff_db = 'GRCh37.87'
species = 'homo_sapiens'
vep_cache_version = '99'
}
'smallerGRCh37' {
fasta = "${params.genomes_base}/human_g1k_v37_decoy.small.fasta"
known_indels = "${params.genomes_base}/dbsnp_138.b37.small.vcf.gz"
}
'custom' {
fasta = null
}
}
}