This repository has been archived by the owner on Jan 27, 2020. It is now read-only.
forked from nf-core/sarek
-
Notifications
You must be signed in to change notification settings - Fork 7
/
genomes.config
67 lines (66 loc) · 4.15 KB
/
genomes.config
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
/*
* -------------------------------------------------
* Nextflow config file for Sarek
* -------------------------------------------------
* Path to reference files
* -------------------------------------------------
* Imported under Nextflow profiles in
* nextflow.config
* -------------------------------------------------
* Defines reference genomes, using paths
* Can be used by any config that customises the base
* path using $params.genome_base / --genome_base
* -------------------------------------------------
*/
params {
genomes {
'GRCh37' {
acLoci = "${params.genome_base}/1000G_phase3_20130502_SNP_maf0.3.loci"
acLociGC = "${params.genome_base}/1000G_phase3_20130502_SNP_maf0.3.loci.gc"
bwaIndex = "${params.genome_base}/human_g1k_v37_decoy.fasta.{amb,ann,bwt,pac,sa}"
dbsnp = "${params.genome_base}/dbsnp_138.b37.vcf"
dbsnpIndex = "${params.genome_base}/dbsnp_138.b37.vcf.idx"
genomeDict = "${params.genome_base}/human_g1k_v37_decoy.dict"
genomeFile = "${params.genome_base}/human_g1k_v37_decoy.fasta"
genomeIndex = "${params.genome_base}/human_g1k_v37_decoy.fasta.fai"
intervals = "${params.genome_base}/wgs_calling_regions_CAW.list"
knownIndels = "${params.genome_base}/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf"
knownIndelsIndex = "${params.genome_base}/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.idx"
snpeffDb = "GRCh37.75"
vepCacheVersion = "96"
}
'GRCh38' {
acLoci = "${params.genome_base}/1000G_phase3_GRCh38_maf0.3.loci"
acLociGC = "${params.genome_base}/1000G_phase3_GRCh38_maf0.3.loci.gc"
bwaIndex = "${params.genome_base}/Homo_sapiens_assembly38.fasta.64.{alt,amb,ann,bwt,pac,sa}"
dbsnp = "${params.genome_base}/dbsnp_146.hg38.vcf.gz"
dbsnpIndex = "${params.genome_base}/dbsnp_146.hg38.vcf.gz.tbi"
genomeDict = "${params.genome_base}/Homo_sapiens_assembly38.dict"
genomeFile = "${params.genome_base}/Homo_sapiens_assembly38.fasta"
genomeIndex = "${params.genome_base}/Homo_sapiens_assembly38.fasta.fai"
intervals = "${params.genome_base}/wgs_calling_regions.hg38.bed"
knownIndels = "${params.genome_base}/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz"
knownIndelsIndex = "${params.genome_base}/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi"
snpeffDb = "GRCh38.86"
vepCacheVersion = "96"
// This a nasty-looking list of allele-frequencies files. Add/remove files to match to your sets
//AF_files = "${params.genome_base}/{00-All.dbsnp_151.hg38.CAF.TOPMED.alternate.allele.freq,hapmap_3.3_grch38_pop_stratified_af.HMAF,SweGen_hg38_stratified.SWAF}.vcf"
//AF_indexes = "${params.genome_base}/{00-All.dbsnp_151.hg38.CAF.TOPMED.alternate.allele.freq,hapmap_3.3_grch38_pop_stratified_af.HMAF,SweGen_hg38_stratified.SWAF}.vcf.idx"
}
'smallGRCh37' {
acLoci = "${params.genome_base}/1000G_phase3_20130502_SNP_maf0.3.small.loci"
acLociGC = "${params.genome_base}/1000G_phase3_20130502_SNP_maf0.3.small.loci.gc"
bwaIndex = "${params.genome_base}/human_g1k_v37_decoy.small.fasta.{amb,ann,bwt,pac,sa}"
dbsnp = "${params.genome_base}/dbsnp_138.b37.small.vcf"
dbsnpIndex = "${params.genome_base}/dbsnp_138.b37.small.vcf.idx"
genomeDict = "${params.genome_base}/human_g1k_v37_decoy.small.dict"
genomeFile = "${params.genome_base}/human_g1k_v37_decoy.small.fasta"
genomeIndex = "${params.genome_base}/human_g1k_v37_decoy.small.fasta.fai"
intervals = "${params.genome_base}/small.intervals"
knownIndels = "${params.genome_base}/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.small.vcf"
knownIndelsIndex = "${params.genome_base}/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.small.vcf.idx"
snpeffDb = "GRCh37.75"
vepCacheVersion = "96"
}
}
}