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Add monkeypox genome files to viralrecon genome config file

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Harshil Patel 2022-08-24 12:13:17 +01:00
parent 49c71e0c28
commit 8dcfcfd856
1 changed files with 23 additions and 0 deletions
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23
conf/pipeline/viralrecon/genomes.config
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@ -8,6 +8,8 @@
params { params {
// Genome reference file paths // Genome reference file paths
genomes { genomes {
// SARS-CoV-2
'NC_045512.2' { 'NC_045512.2' {
// This version of the reference has been kept here for backwards compatibility. // 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 // Please use 'MN908947.3' if possible because all primer sets are available / have been pre-prepared relative to that assembly
@ -18,6 +20,8 @@ params {
nextclade_dataset_reference = 'MN908947' nextclade_dataset_reference = 'MN908947'
nextclade_dataset_tag = '2022-06-14T12:00:00Z' nextclade_dataset_tag = '2022-06-14T12:00:00Z'
} }
// SARS-CoV-2
'MN908947.3' { 'MN908947.3' {
fasta = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.fna.gz' 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' gff = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz'
@ -66,5 +70,24 @@ params {
} }
} }
} }
// Monkeypox
'NC_063383.1' {
fasta = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/NC_063383.1/GCA_014621545.1_ASM1462154v1_genomic.220824.fna.gz'
gff = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/NC_063383.1/GCA_014621545.1_ASM1462154v1_genomic.220824.gff.gz'
}
// Monkeypox
'ON563414.3' {
fasta = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/ON563414.3/GCA_023516015.3_ASM2351601v1_genomic.220824.fna.gz'
gff = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/ON563414.3/GCA_023516015.3_ASM2351601v1_genomic.220824.gff.gz'
}
// Monkeypox
'MT903344.1' {
fasta = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MT903344.1/GCA_014621585.1_ASM1462158v1_genomic.220824.fna.gz'
gff = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MT903344.1/GCA_014621585.1_ASM1462158v1_genomic.220824.gff.gz'
}
} }
} }