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