Merge branch 'nextclade-bump' into 'dev'

updating nextclade data for Omicron See merge request epi2melabs/workflow-containers/wf-artic!77
epi2me-labs · Dec 2, 2021 · 35c2630 · 35c2630
2 parents cef394b + 78e6a30
commit 35c2630
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,10 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v0.3.8]
+### Fixed
+- Nextclade data was out of date, now calls Omicron
+
 ## [v0.3.7]
 ### Fixed
 - Pangolin update step now checks for internet connection

diff --git a/data/nextclade/primers.csv b/data/nextclade/primers.csv
@@ -0,0 +1,37 @@
+Country (Institute),Target,Oligonucleotide,Sequence
+Charité (Germany),RdRp,Charité_RdRp_F,GTGARATGGTCATGTGTGGCGG
+Charité (Germany),RdRp,Charité_S_RdRp_P,CAGGTGGAACCTCATCAGGAGATGC
+Charité (Germany),RdRp,Charité_RdRp_R,CARATGTTAAASACACTATTAGCATA
+Charité (Germany),E,Charité_E_F,ACAGGTACGTTAATAGTTAATAGCGT
+Charité (Germany),E,Charité_E_P,ACACTAGCCATCCTTACTGCGCTTCG
+Charité (Germany),E,Charité_E_R,ATATTGCAGCAGTACGCACACA
+Charité (Germany),N,Charité_N_F,CACATTGGCACCCGCAATC
+Charité (Germany),N,Charité_N_P,ACTTCCTCAAGGAACAACATTGCCA
+Charité (Germany),N,Charité_N_R,GAGGAACGAGAAGAGGCTTG
+HKU (Hong Kong),ORF1b-nsp14,HKU_ORF_F,TGGGGYTTTACRGGTAACCT
+HKU (Hong Kong),ORF1b-nsp14,HKU_ORF_P,TAGTTGTGATGCWATCATGACTAG
+HKU (Hong Kong),ORF1b-nsp14,HKU_ORF_R,AACRCGCTTAACAAAGCACTC
+HKU (Hong Kong),N,HKU_N_F,TAATCAGACAAGGAACTGATTA
+HKU (Hong Kong),N,HKU_N_P,GCAAATTGTGCAATTTGCGG
+HKU (Hong Kong),N,HKU_N_R,CGAAGGTGTGACTTCCATG
+China CDC (China),N,ChinaCDC_N_F,GGGGAACTTCTCCTGCTAGAAT
+China CDC (China),N,ChinaCDC_N_P,TTGCTGCTGCTTGACAGATT
+China CDC (China),N,ChinaCDC_N_R,CAGACATTTTGCTCTCAAGCTG
+China CDC (China),ORF1ab-nsp10,ChinaCDC_ORF_F,CCCTGTGGGTTTTACACTTAA
+China CDC (China),ORF1ab-nsp10,ChinaCDC_ORF_P,CCGTCTGCGGTATGTGGAAAGGTTATGG
+China CDC (China),ORF1ab-nsp10,ChinaCDC_ORF_R,ACGATTGTGCATCAGCTGA
+US CDC (United States),N1,USCDC_N1_F,GACCCCAAAATCAGCGAAAT
+US CDC (United States),N1,USCDC_N1_P,ACCCCGCATTACGTTTGGTGGACC
+US CDC (United States),N1,USCDC_N1_R,TCTGGTTACTGCCAGTTGAATCTG
+US CDC (United States),N2,USCDC_N2_F,TTACAAACATTGGCCGCAAA
+US CDC (United States),N2,USCDC_N2_P,ACAATTTGCCCCCAGCGCTTCAG
+US CDC (United States),N2,USCDC_N2_R,GCGCGACATTCCGAAGAA
+US CDC (United States),N3,USCDC_N3_F,GGGAGCCTTGAATACACCAAAA
+US CDC (United States),N3,USCDC_N3_P,AYCACATTGGCACCCGCAATCCTG
+US CDC (United States),N3,USCDC_N3_R,TGTAGCACGATTGCAGCATTG
+"Institut Pasteur, Paris (France)",RdRp,Pasteur_IP2_F,ATGAGCTTAGTCCTGTTG
+"Institut Pasteur, Paris (France)",RdRp,Pasteur_IP2_P,AGATGTCTTGTGCTGCCGGTA
+"Institut Pasteur, Paris (France)",RdRp,Pasteur_IP2_R,CTCCCTTTGTTGTGTTGT
+"Institut Pasteur, Paris (France)",RdRp,Pasteur_IP4_F,GGTAACTGGTATGATTTCG
+"Institut Pasteur, Paris (France)",RdRp,Pasteur_IP4_P,TCATACAAACCACGCCAGG
+"Institut Pasteur, Paris (France)",RdRp,Pasteur_IP4_R,CTGGTCAAGGTTAATATAGG
diff --git a/data/nextclade/qc.json b/data/nextclade/qc.json
@@ -21,13 +21,70 @@
     "mixedSitesThreshold": 10
   },
   "frameShifts": {
-    "enabled": true
+    "enabled": true,
+    "ignoredFrameShifts": [
+      { "geneName": "ORF3a", "codonRange": {"begin": 256, "end": 276 } },
+      { "geneName": "ORF3a", "codonRange": {"begin": 258, "end": 276 } },
+      { "geneName": "ORF6", "codonRange": {"begin": 21, "end": 62 } },
+      { "geneName": "ORF6", "codonRange": {"begin": 29, "end": 62 } },
+      { "geneName": "ORF6", "codonRange": {"begin": 30, "end": 62 } },
+      { "geneName": "ORF6", "codonRange": {"begin": 37, "end": 62 } },
+      { "geneName": "ORF7a", "codonRange": {"begin": 53, "end": 122 } },
+      { "geneName": "ORF7a", "codonRange": {"begin": 61, "end": 122 } },
+      { "geneName": "ORF7a", "codonRange": {"begin": 62, "end": 122 } },
+      { "geneName": "ORF7a", "codonRange": {"begin": 63, "end": 122 } },
+      { "geneName": "ORF7a", "codonRange": {"begin": 64, "end": 122 } },
+      { "geneName": "ORF7a", "codonRange": {"begin": 65, "end": 122 } },
+      { "geneName": "ORF7a", "codonRange": {"begin": 68, "end": 122 } },
+      { "geneName": "ORF7a", "codonRange": {"begin": 71, "end": 122 } },
+      { "geneName": "ORF7a", "codonRange": {"begin": 74, "end": 122 } },
+      { "geneName": "ORF7a", "codonRange": {"begin": 75, "end": 122 } },
+      { "geneName": "ORF7a", "codonRange": {"begin": 76, "end": 122 } },
+      { "geneName": "ORF7a", "codonRange": {"begin": 77, "end": 122 } },
+      { "geneName": "ORF7a", "codonRange": {"begin": 78, "end": 122 } },
+      { "geneName": "ORF7a", "codonRange": {"begin": 80, "end": 122 } },
+      { "geneName": "ORF7a", "codonRange": {"begin": 81, "end": 122 } },
+      { "geneName": "ORF7a", "codonRange": {"begin": 82, "end": 122 } },
+      { "geneName": "ORF7a", "codonRange": {"begin": 84, "end": 122 } },
+      { "geneName": "ORF7a", "codonRange": {"begin": 100, "end": 122 } },
+      { "geneName": "ORF7a", "codonRange": {"begin": 101, "end": 122 } },
+      { "geneName": "ORF7a", "codonRange": {"begin": 102, "end": 122 } },
+      { "geneName": "ORF7a", "codonRange": {"begin": 103, "end": 122 } },
+      { "geneName": "ORF7a", "codonRange": {"begin": 109, "end": 122 } },
+      { "geneName": "ORF7a", "codonRange": {"begin": 116, "end": 122 } },
+      { "geneName": "ORF7b", "codonRange": {"begin": 41, "end": 44 } },
+      { "geneName": "ORF7b", "codonRange": {"begin": 42, "end": 44 } },
+      { "geneName": "ORF8", "codonRange": {"begin": 45, "end": 122 } },
+      { "geneName": "ORF8", "codonRange": {"begin": 67, "end": 122 } },
+      { "geneName": "ORF8", "codonRange": {"begin": 107, "end": 122 } },
+      { "geneName": "ORF8", "codonRange": {"begin": 118, "end": 120 } },
+      { "geneName": "ORF8", "codonRange": {"begin": 119, "end": 122 } },
+      { "geneName": "ORF8", "codonRange": {"begin": 120, "end": 122 } }
+    ]
   },
   "stopCodons": {
     "enabled": true,
     "ignoredStopCodons": [
-      {"geneName": "ORF8", "codon": 26},
-      {"geneName": "ORF8", "codon": 67}
+      { "geneName": "ORF3a", "codon": 253 },
+      { "geneName": "ORF7a", "codon": 37 },
+      { "geneName": "ORF7a", "codon": 40 },
+      { "geneName": "ORF7a", "codon": 61 },
+      { "geneName": "ORF7a", "codon": 75 },
+      { "geneName": "ORF7a", "codon": 76 },
+      { "geneName": "ORF7a", "codon": 89 },
+      { "geneName": "ORF7a", "codon": 93 },
+      { "geneName": "ORF7a", "codon": 94 },
+      { "geneName": "ORF7a", "codon": 120 },
+      { "geneName": "ORF7b", "codon": 32 },
+      { "geneName": "ORF7b", "codon": 38 },
+      { "geneName": "ORF8", "codon": 17 },
+      { "geneName": "ORF8", "codon": 18 },
+      { "geneName": "ORF8", "codon": 26 },
+      { "geneName": "ORF8", "codon": 58 },
+      { "geneName": "ORF8", "codon": 63 },
+      { "geneName": "ORF8", "codon": 67 },
+      { "geneName": "ORF8", "codon": 105 },
+      { "geneName": "ORF8", "codon": 109 }
     ]
   }
 }