From f283dfb2dcfec79b120953c9ee7d6e3ab4aec695 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Mon, 15 Feb 2021 16:58:30 +0000 Subject: [PATCH 1/2] Add ARTIC primer sets to genome config --- conf/pipeline/viralrecon/genomes.config | 34 +++++++++++++++++++++---- 1 file changed, 29 insertions(+), 5 deletions(-) diff --git a/conf/pipeline/viralrecon/genomes.config b/conf/pipeline/viralrecon/genomes.config index d889460..d321e57 100644 --- a/conf/pipeline/viralrecon/genomes.config +++ b/conf/pipeline/viralrecon/genomes.config @@ -4,17 +4,41 @@ * ------------------------------------------------- * Defines viral reference genomes for all environments. */ - + params { // Genome reference file paths genomes { '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" - gff = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.gff.gz" + // 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://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' { - 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" + 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' + 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' + } + } + } } } } From 9d500cf6790e593b91fa9e76d647e355a863009b Mon Sep 17 00:00:00 2001 From: drpatelh Date: Mon, 15 Feb 2021 17:02:26 +0000 Subject: [PATCH 2/2] Reorder params --- conf/pipeline/viralrecon/genomes.config | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/conf/pipeline/viralrecon/genomes.config b/conf/pipeline/viralrecon/genomes.config index d321e57..6321e8f 100644 --- a/conf/pipeline/viralrecon/genomes.config +++ b/conf/pipeline/viralrecon/genomes.config @@ -20,22 +20,22 @@ params { 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' + primer_bed = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V1/nCoV-2019.primer.bed' + scheme = 'nCoV-2019' } '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' + primer_bed = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V2/nCoV-2019.primer.bed' + scheme = 'nCoV-2019' } '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' + primer_bed = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.primer.bed' + scheme = 'nCoV-2019' } } }