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Merge pull request #418 from maxulysse/dev_tbi
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Fix: issues with known_sites channels
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@maxulysse
maxulysse authored Aug 3, 2021
2 parents 4d5f3dc + 4217d0a commit 474706c
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Showing 7 changed files with 347 additions and 334 deletions.
138 changes: 69 additions & 69 deletions conf/genomes.config
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Original file line number Diff line number Diff line change
Expand Up @@ -10,89 +10,89 @@
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'
vep_genome = 'GRCh37'
vep_species = 'homo_sapiens'
vep_cache_version = '104'
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_tbi = "${params.genomes_base}/dbsnp_138.b37.vcf.idx"
dict = "${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 = "${params.genomes_base}/gnomAD.r2.1.1.GRCh37.PASS.AC.AF.only.vcf.gz"
germline_resource_tbi = "${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_tbi = "${params.genomes_base}/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.idx"
mappability = "${params.genomes_base}/out100m2_hg19.gem"
snpeff_db = 'GRCh37.75'
vep_genome = 'GRCh37'
vep_species = 'homo_sapiens'
vep_cache_version = '104'
}
'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 = 'GRCh38.99'
vep_genome = 'GRCh38'
vep_species = 'homo_sapiens'
vep_cache_version = '104'
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_tbi = "${params.genomes_base}/dbsnp_146.hg38.vcf.gz.tbi"
dict = "${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 = "${params.genomes_base}/gnomAD.r2.1.1.GRCh38.PASS.AC.AF.only.vcf.gz"
germline_resource_tbi = "${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_tbi = "${params.genomes_base}/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi"
mappability = "${params.genomes_base}/out100m2_hg38.gem"
snpeff_db = 'GRCh38.99'
vep_genome = 'GRCh38'
vep_species = 'homo_sapiens'
vep_cache_version = '104'
}
'minimalGRCh37' {
fasta = "${params.genomes_base}/human_g1k_v37_decoy.small.fasta"
fasta = "${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 = "${params.genomes_base}/Mills_1000G_gold_standard_and_1000G_phase1.indels.b37.small.vcf.gz"
snpeff_db = 'GRCh37.75'
vep_genome = 'GRCh37'
vep_species = 'homo_sapiens'
vep_cache_version = '104'
dbsnp = "${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 = 'GRCh37.75'
vep_genome = 'GRCh37'
vep_species = 'homo_sapiens'
vep_cache_version = '104'
}
'smallerGRCh37' {
fasta = "${params.genomes_base}/human_g1k_v37_decoy.small.fasta"
known_indels = "${params.genomes_base}/dbsnp_138.b37.small.vcf.gz"
fasta = "${params.genomes_base}/human_g1k_v37_decoy.small.fasta"
known_indels = "${params.genomes_base}/dbsnp_138.b37.small.vcf.gz"
}
'smallGRCh38' {
dbsnp = "${params.genomes_base}/dbsnp_146_hg38_chr20_tso-only.vcf.gz"
fasta = "${params.genomes_base}/Homo_sapiens_assembly38_chr20.fasta"
known_indels = "${params.genomes_base}/Mills_and_1000G_gold_standard_indels_hg38_chr20.vcf.gz"
snpeff_db = 'GRCh38.99'
vep_genome = 'GRCh38'
vep_species = 'homo_sapiens'
vep_cache_version = '99'
dbsnp = "${params.genomes_base}/dbsnp_146_hg38_chr20_tso-only.vcf.gz"
fasta = "${params.genomes_base}/Homo_sapiens_assembly38_chr20.fasta"
known_indels = "${params.genomes_base}/Mills_and_1000G_gold_standard_indels_hg38_chr20.vcf.gz"
snpeff_db = 'GRCh38.99'
vep_genome = 'GRCh38'
vep_species = 'homo_sapiens'
vep_cache_version = '99'
}
'custom' {
fasta = null
fasta = null
}
'small_hg38' {
dbsnp = "${params.genomes_base}/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz"
fasta = "${params.genomes_base}/data/genomics/homo_sapiens/genome/genome.fasta"
fasta_fai = "${params.genomes_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai"
germline_resource = "${params.genomes_base}/data/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz"
known_indels = "${params.genomes_base}/data/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz"
snpeff_db = 'GRCh38.99'
vep_genome = 'GRCh38'
vep_species = 'homo_sapiens'
vep_cache_version = '104'
dbsnp = "${params.genomes_base}/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz"
fasta = "${params.genomes_base}/data/genomics/homo_sapiens/genome/genome.fasta"
fasta_fai = "${params.genomes_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai"
germline_resource = "${params.genomes_base}/data/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz"
known_indels = "${params.genomes_base}/data/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz"
snpeff_db = 'GRCh38.99'
vep_genome = 'GRCh38'
vep_species = 'homo_sapiens'
vep_cache_version = '104'
}
}
}
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