Merge branch 'nextclade' into 'dev'

update nextclade cli to latest C++ version

See merge request epi2melabs/workflow-containers/wf-artic!54

data/nextclade/genemap.gff

@@ -0,0 +1,16 @@
+# Gene map (genome annotation) of SARS-CoV-2 in GFF format.
+# For gene map purpses we only need some of the columns. We substitute unused values with "." as per GFF spec.
+# See GFF format reference at https://www.ensembl.org/info/website/upload/gff.html
+# seqname	source	feature	start	end	score	strand	frame	attribute
+.	.	gene	26245	26472	.	+	.	 gene_name=E
+.	.	gene	26523	27191	.	+	.	 gene_name=M
+.	.	gene	28274	29533	.	+	.	 gene_name=N
+.	.	gene	266	13468	.	+	.	 gene_name=ORF1a
+.	.	gene	13468	21555	.	+	.	 gene_name=ORF1b
+.	.	gene	25393	26220	.	+	.	 gene_name=ORF3a
+.	.	gene	27202	27387	.	+	.	 gene_name=ORF6
+.	.	gene	27394	27759	.	+	.	 gene_name=ORF7a
+.	.	gene	27756	27887	.	+	.	 gene_name=ORF7b
+.	.	gene	27894	28259	.	+	.	 gene_name=ORF8
+.	.	gene	28284	28577	.	+	.	 gene_name=ORF9b
+.	.	gene	21563	25384	.	+	.	 gene_name=S

data/nextclade/qc.json

@@ -0,0 +1,33 @@
+{
+  "schemaVersion": "1.2.0",
+  "privateMutations": {
+    "enabled": true,
+    "typical": 8,
+    "cutoff": 24
+  },
+  "missingData": {
+    "enabled": true,
+    "missingDataThreshold": 2700,
+    "scoreBias": 300
+  },
+  "snpClusters": {
+    "enabled": true,
+    "windowSize": 100,
+    "clusterCutOff": 6,
+    "scoreWeight": 50
+  },
+  "mixedSites": {
+    "enabled": true,
+    "mixedSitesThreshold": 10
+  },
+  "frameShifts": {
+    "enabled": true
+  },
+  "stopCodons": {
+    "enabled": true,
+    "ignoredStopCodons": [
+      {"geneName": "ORF8", "codon": 26},
+      {"geneName": "ORF8", "codon": 67}
+    ]
+  }
+}

data/nextclade/tag.json

@@ -0,0 +1,32 @@
+{
+  "comment": "Initial release",
+  "compatibility": {
+    "nextcladeCli": {
+      "max": null,
+      "min": "1.3.0"
+    },
+    "nextcladeWeb": {
+      "max": null,
+      "min": "1.6.0"
+    }
+  },
+  "defaultRef": "MN908947",
+  "enabled": true,
+  "files": {
+    "geneMap": "genemap.gff",
+    "primers": "primers.csv",
+    "qc": "qc.json",
+    "reference": "reference.fasta",
+    "sequences": "sequences.fasta",
+    "tree": "tree.json"
+  },
+  "metadata": {},
+  "name": "sars-cov-2",
+  "nameFriendly": "SARS-CoV-2",
+  "reference": {
+    "accession": "MN908947",
+    "source": "genbank",
+    "strainName": "Wuhan-Hu-1/2019"
+  },
+  "tag": "2021-06-25T00:00:00Z"
+}