mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-11-27 01:59:56 +00:00
70 lines
4.8 KiB
Text
70 lines
4.8 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'
|
|
nextclade_dataset = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/nextclade_sars-cov-2_MN908947_2022-01-18T12_00_00Z.tar.gz'
|
|
nextclade_dataset_name = 'sars-cov-2'
|
|
nextclade_dataset_reference = 'MN908947'
|
|
nextclade_dataset_tag = '2022-01-18T12:00:00Z'
|
|
}
|
|
'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'
|
|
nextclade_dataset = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/nextclade_sars-cov-2_MN908947_2022-01-18T12_00_00Z.tar.gz'
|
|
nextclade_dataset_name = 'sars-cov-2'
|
|
nextclade_dataset_reference = 'MN908947'
|
|
nextclade_dataset_tag = '2022-01-18T12:00:00Z'
|
|
primer_sets {
|
|
artic {
|
|
'1' {
|
|
fasta = 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/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/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V1/nCoV-2019.primer.bed'
|
|
scheme = 'nCoV-2019'
|
|
}
|
|
'2' {
|
|
fasta = 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/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/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V2/nCoV-2019.primer.bed'
|
|
scheme = 'nCoV-2019'
|
|
}
|
|
'3' {
|
|
fasta = 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/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/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V3/nCoV-2019.primer.bed'
|
|
scheme = 'nCoV-2019'
|
|
}
|
|
'4' {
|
|
fasta = 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V4/SARS-CoV-2.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/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V4/SARS-CoV-2.scheme.bed'
|
|
scheme = 'SARS-CoV-2'
|
|
}
|
|
'4.1' {
|
|
fasta = 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V4.1/SARS-CoV-2.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/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V4.1/SARS-CoV-2.scheme.bed'
|
|
scheme = 'SARS-CoV-2'
|
|
}
|
|
'1200' {
|
|
fasta = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/primer_schemes/artic/nCoV-2019/V1200/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/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/primer_schemes/artic/nCoV-2019/V1200/nCoV-2019.bed'
|
|
scheme = 'nCoV-2019'
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|