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Add ARTIC primer sets to genome config

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drpatelh 2021-02-15 16:58:30 +00:00
parent 86566ddd3b
commit f283dfb2dc
1 changed files with 29 additions and 5 deletions
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34
conf/pipeline/viralrecon/genomes.config
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@ -4,17 +4,41 @@
* ------------------------------------------------- * -------------------------------------------------
* Defines viral reference genomes for all environments. * Defines viral reference genomes for all environments.
*/ */
params { params {
// Genome reference file paths // Genome reference file paths
genomes { genomes {
'NC_045512.2' { 'NC_045512.2' {
fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.fna.gz" // This version of the reference has been kept here for backwards compatibility.
gff = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.gff.gz" // Please use 'MN908947.3' if possible because all primer sets are available / have been pre-prepared relative to that assembly
fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.fna.gz'
gff = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.gff.gz'
} }
'MN908947.3' { 'MN908947.3' {
fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.fna.gz" fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.fna.gz'
gff = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz" gff = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz'
primer_sets {
artic {
'1' {
scheme = 'nCoV-2019'
primer_bed = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V1/nCoV-2019.primer.bed'
fasta = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V1/nCoV-2019.reference.fasta'
gff = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz'
}
'2' {
scheme = 'nCoV-2019'
primer_bed = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V2/nCoV-2019.primer.bed'
fasta = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V2/nCoV-2019.reference.fasta'
gff = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz'
}
'3' {
scheme = 'nCoV-2019'
primer_bed = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.primer.bed'
fasta = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.reference.fasta'
gff = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz'
}
}
}
} }
} }
} }