From 93cfc48afd7bf36c9df939847f5275ff31fcec0d Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Mon, 21 Jun 2021 21:04:16 +0100 Subject: [PATCH] Add ARTIC v4 primers to genomes config --- conf/pipeline/viralrecon/genomes.config | 18 ++++++++++++------ 1 file changed, 12 insertions(+), 6 deletions(-) diff --git a/conf/pipeline/viralrecon/genomes.config b/conf/pipeline/viralrecon/genomes.config index 27f7162..e7b1c2f 100644 --- a/conf/pipeline/viralrecon/genomes.config +++ b/conf/pipeline/viralrecon/genomes.config @@ -20,23 +20,29 @@ params { primer_sets { artic { '1' { - fasta = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V1/nCoV-2019.reference.fasta' + 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/primer-schemes/raw/master/nCoV-2019/V1/nCoV-2019.primer.bed' + 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/primer-schemes/raw/master/nCoV-2019/V2/nCoV-2019.reference.fasta' + 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/primer-schemes/raw/master/nCoV-2019/V2/nCoV-2019.primer.bed' + 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/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.reference.fasta' + 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/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.primer.bed' + 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' + } } } }