mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-11-29 02:49:55 +00:00
44 lines
2.5 KiB
Text
44 lines
2.5 KiB
Text
/*
|
|
* -------------------------------------------------
|
|
* nfcore/viralrecon custom profile Nextflow config file
|
|
* -------------------------------------------------
|
|
* Defines viral reference genomes for all environments.
|
|
*/
|
|
|
|
params {
|
|
// Genome reference file paths
|
|
genomes {
|
|
'NC_045512.2' {
|
|
// This version of the reference has been kept here for backwards compatibility.
|
|
// Please use 'MN908947.3' if possible because all primer sets are available / have been pre-prepared relative to that assembly
|
|
fasta = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.fna.gz'
|
|
gff = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.gff.gz'
|
|
}
|
|
'MN908947.3' {
|
|
fasta = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.fna.gz'
|
|
gff = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz'
|
|
primer_sets {
|
|
artic {
|
|
'1' {
|
|
fasta = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V1/nCoV-2019.reference.fasta'
|
|
gff = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz'
|
|
primer_bed = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V1/nCoV-2019.primer.bed'
|
|
scheme = 'nCoV-2019'
|
|
}
|
|
'2' {
|
|
fasta = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V2/nCoV-2019.reference.fasta'
|
|
gff = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz'
|
|
primer_bed = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V2/nCoV-2019.primer.bed'
|
|
scheme = 'nCoV-2019'
|
|
}
|
|
'3' {
|
|
fasta = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.reference.fasta'
|
|
gff = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz'
|
|
primer_bed = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.primer.bed'
|
|
scheme = 'nCoV-2019'
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|