From 19316ce8527fb1f1f46c842c65116d933779e0bd Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Thu, 9 Apr 2020 13:40:35 +0200 Subject: [PATCH 1/3] add viralrecon specific config --- pipeline/viralrecon.config | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 pipeline/viralrecon.config diff --git a/pipeline/viralrecon.config b/pipeline/viralrecon.config new file mode 100644 index 0000000..3aa23af --- /dev/null +++ b/pipeline/viralrecon.config @@ -0,0 +1,16 @@ +/* + * ------------------------------------------------- + * nfcore/viralrecon custom profile Nextflow config file + * ------------------------------------------------- + * 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/reference/NC_045512.2.fasta.gz" + gff = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/reference/NC_045512.2.gff.gz" + } + } +} From 290d0a21803dc2baee983aa358e7260b97de642c Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 9 Apr 2020 13:31:20 +0100 Subject: [PATCH 2/3] Update pipeline/viralrecon.config --- pipeline/viralrecon.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipeline/viralrecon.config b/pipeline/viralrecon.config index 3aa23af..afe373c 100644 --- a/pipeline/viralrecon.config +++ b/pipeline/viralrecon.config @@ -9,7 +9,7 @@ params { // Genome reference file paths genomes { 'NC_045512.2' { - fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/reference/NC_045512.2.fasta.gz" + fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/NC_045512.2/NC_045512.2.fasta.gz" gff = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/reference/NC_045512.2.gff.gz" } } From 4fd9b73cecef10a2e863d88b5bd753ec5a4fd4a7 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 9 Apr 2020 13:31:39 +0100 Subject: [PATCH 3/3] Update pipeline/viralrecon.config --- pipeline/viralrecon.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipeline/viralrecon.config b/pipeline/viralrecon.config index afe373c..45c8247 100644 --- a/pipeline/viralrecon.config +++ b/pipeline/viralrecon.config @@ -10,7 +10,7 @@ params { genomes { 'NC_045512.2' { fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/NC_045512.2/NC_045512.2.fasta.gz" - gff = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/reference/NC_045512.2.gff.gz" + gff = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/NC_045512.2/NC_045512.2.gff.gz" } } }