Merge pull request #30 from quick-lab/staging

Staging
quick-lab · May 14, 2024 · bc97b2f · bc97b2f
2 parents 5a7d12d + 856335f
commit bc97b2f
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Showing 93 changed files with 2,708 additions and 2,296 deletions.
diff --git a/index.json b/index.json
diff --git a/primerschemes/artic-measles/400/v1.0.0/README.md b/primerschemes/artic-measles/400/v1.0.0/README.md
@@ -1,5 +1,7 @@
 # artic-measles 400bp v1.0.0
 
+[primalscheme labs](https://labs.primalscheme.com/detail/artic-measles/400/v1.0.0)
+
 ## Description
 
 A pan Measles morbillivirus scheme. All full length genomes have been downloaded and phylogenicly downsampled to 0.95 RTL.
@@ -15,8 +17,8 @@ A pan Measles morbillivirus scheme. All full length genomes have been downloaded
     "ampliconsize": 400,
     "schemeversion": "v1.0.0",
     "schemename": "artic-measles",
-    "primer_bed_md5": "b8b903356d4c6bd4dc03af04f3a18222",
-    "reference_fasta_md5": "2c3dd74742a333dffb50bcfbd158bfbd",
+    "primer_bed_md5": "b75c16322b1e1c5e606917b5653c01f1",
+    "reference_fasta_md5": "64a52bcc7c18986db1c11813db518390",
     "status": "tested",
     "citations": [],
     "authors": [
@@ -29,16 +31,24 @@ A pan Measles morbillivirus scheme. All full length genomes have been downloaded
     ],
     "license": "CC BY-SA 4.0",
     "primerclass": "primerschemes",
-    "infoschema": "v1.3.0",
+    "infoschema": "v2.0.0",
     "articbedversion": "v3.0",
-    "description": "A pan Measles morbillivirus scheme. All full length genomes have been downloaded and phylogenicly downsampled to 0.95 RTL.",
-    "derivedfrom": null,
     "collections": [
-        "WASTE-WATER",
         "QUICK-LAB",
         "WHOLE-GENOME",
+        "WASTE-WATER",
         "ARTIC"
-    ]
+    ],
+    "links": {
+        "protocals": [],
+        "validation": [],
+        "homepage": [],
+        "vendors": [],
+        "misc": []
+    },
+    "description": "A pan Measles morbillivirus scheme. All full length genomes have been downloaded and phylogenicly downsampled to 0.95 RTL.",
+    "derivedfrom": null,
+    "contactinfo": null
 }
 ```
 

diff --git a/primerschemes/artic-measles/400/v1.0.0/info.json b/primerschemes/artic-measles/400/v1.0.0/info.json
@@ -2,8 +2,8 @@
     "ampliconsize": 400,
     "schemeversion": "v1.0.0",
     "schemename": "artic-measles",
-    "primer_bed_md5": "b8b903356d4c6bd4dc03af04f3a18222",
-    "reference_fasta_md5": "2c3dd74742a333dffb50bcfbd158bfbd",
+    "primer_bed_md5": "b75c16322b1e1c5e606917b5653c01f1",
+    "reference_fasta_md5": "64a52bcc7c18986db1c11813db518390",
     "status": "tested",
     "citations": [],
     "authors": [
@@ -16,14 +16,22 @@
     ],
     "license": "CC BY-SA 4.0",
     "primerclass": "primerschemes",
-    "infoschema": "v1.3.0",
+    "infoschema": "v2.0.0",
     "articbedversion": "v3.0",
-    "description": "A pan Measles morbillivirus scheme. All full length genomes have been downloaded and phylogenicly downsampled to 0.95 RTL.",
-    "derivedfrom": null,
     "collections": [
-        "WASTE-WATER",
         "QUICK-LAB",
         "WHOLE-GENOME",
+        "WASTE-WATER",
         "ARTIC"
-    ]
+    ],
+    "links": {
+        "protocals": [],
+        "validation": [],
+        "homepage": [],
+        "vendors": [],
+        "misc": []
+    },
+    "description": "A pan Measles morbillivirus scheme. All full length genomes have been downloaded and phylogenicly downsampled to 0.95 RTL.",
+    "derivedfrom": null,
+    "contactinfo": null
 }
diff --git a/primerschemes/artic-measles/400/v1.0.0/primer.bed b/primerschemes/artic-measles/400/v1.0.0/primer.bed
@@ -372,4 +372,4 @@ NC_001498.1	15858	15888	177e6ebb_46_RIGHT_3	1	-	CAAAGCTGGGAATAGAAACTTCGTATTTTC
 NC_001498.1	15858	15887	177e6ebb_46_RIGHT_4	1	-	CAAAGCTGGGAATAGAACTTCGTATTTTC
 NC_001498.1	15858	15887	177e6ebb_46_RIGHT_5	1	-	CAAGCTGGGAATAGAAACTTCGTATTTTC
 NC_001498.1	15858	15889	177e6ebb_46_RIGHT_6	1	-	GACAAACTGGGAATAGAAACTTCGTATTTTC
-NC_001498.1	15858	15889	177e6ebb_46_RIGHT_7	1	-	GACAAAGTGGGAATAGAAACTTCGTATTTTC
+NC_001498.1	15858	15889	177e6ebb_46_RIGHT_7	1	-	GACAAAGTGGGAATAGAAACTTCGTATTTTC
diff --git a/primerschemes/artic-measles/400/v1.0.0/reference.fasta b/primerschemes/artic-measles/400/v1.0.0/reference.fasta
@@ -263,4 +263,4 @@ ATCTCAAGTCCGGTTATCTAGTACTAGACTTACACCAGAATATCTTCGTTAAGAATCTAT
 CCAAGTCAGAGAAACAGATTATTATGACGGGGGGTTTAAAACGTGAGTGGGTTTTTAAGG
 TAACAGTCAAGGAGACCAAAGAATGGTACAAGTTAGTCGGATACAGCGCTCTGATTAAGG
 ATTAATTGGTTGAACTCCGGAACCCTAATCCTGCCCTAGGTAGTTAGGCATTATTTGCAA
-TATATTAAAGAAAACTTTGAAAATACGAAGTTTCTATTCCCAGCTTTGTCTGGT
+TATATTAAAGAAAACTTTGAAAATACGAAGTTTCTATTCCCAGCTTTGTCTGGT
diff --git a/primerschemes/artic-pan-ebola/1000/v1.0.0/README.md b/primerschemes/artic-pan-ebola/1000/v1.0.0/README.md
@@ -1,5 +1,7 @@
 # artic-pan-ebola 1000bp v1.0.0
 
+[primalscheme labs](https://labs.primalscheme.com/detail/artic-pan-ebola/1000/v1.0.0)
+
 ## Overviews
 
 ![NC_006432.1.png](work/NC_006432.1.png)
@@ -11,8 +13,8 @@
     "ampliconsize": 1000,
     "schemeversion": "v1.0.0",
     "schemename": "artic-pan-ebola",
-    "primer_bed_md5": "c58ec3b4d07d24499106fed6501016a9",
-    "reference_fasta_md5": "083c89a1798778fbe94a643d83a6fbb1",
+    "primer_bed_md5": "6b9554c28693b521cfbe2246091c61af",
+    "reference_fasta_md5": "c5432a6813f9a2604ea5e5e2bb94508e",
     "status": "draft",
     "citations": [],
     "authors": [
@@ -25,16 +27,24 @@
     ],
     "license": "CC BY-SA 4.0",
     "primerclass": "primerschemes",
-    "infoschema": "v1.3.0",
+    "infoschema": "v2.0.0",
     "articbedversion": "v3.0",
-    "description": null,
-    "derivedfrom": null,
     "collections": [
-        "CLINAL-ISOLATES",
-        "WHOLE-GENOME",
         "QUICK-LAB",
-        "ARTIC"
-    ]
+        "WHOLE-GENOME",
+        "ARTIC",
+        "CLINAL-ISOLATES"
+    ],
+    "links": {
+        "protocals": [],
+        "validation": [],
+        "homepage": [],
+        "vendors": [],
+        "misc": []
+    },
+    "description": null,
+    "derivedfrom": null,
+    "contactinfo": null
 }
 ```
 

diff --git a/primerschemes/artic-pan-ebola/1000/v1.0.0/info.json b/primerschemes/artic-pan-ebola/1000/v1.0.0/info.json
@@ -2,8 +2,8 @@
     "ampliconsize": 1000,
     "schemeversion": "v1.0.0",
     "schemename": "artic-pan-ebola",
-    "primer_bed_md5": "c58ec3b4d07d24499106fed6501016a9",
-    "reference_fasta_md5": "083c89a1798778fbe94a643d83a6fbb1",
+    "primer_bed_md5": "6b9554c28693b521cfbe2246091c61af",
+    "reference_fasta_md5": "c5432a6813f9a2604ea5e5e2bb94508e",
     "status": "draft",
     "citations": [],
     "authors": [
@@ -16,14 +16,22 @@
     ],
     "license": "CC BY-SA 4.0",
     "primerclass": "primerschemes",
-    "infoschema": "v1.3.0",
+    "infoschema": "v2.0.0",
     "articbedversion": "v3.0",
-    "description": null,
-    "derivedfrom": null,
     "collections": [
-        "CLINAL-ISOLATES",
-        "WHOLE-GENOME",
         "QUICK-LAB",
-        "ARTIC"
-    ]
+        "WHOLE-GENOME",
+        "ARTIC",
+        "CLINAL-ISOLATES"
+    ],
+    "links": {
+        "protocals": [],
+        "validation": [],
+        "homepage": [],
+        "vendors": [],
+        "misc": []
+    },
+    "description": null,
+    "derivedfrom": null,
+    "contactinfo": null
 }
diff --git a/primerschemes/artic-pan-ebola/1000/v1.0.0/primer.bed b/primerschemes/artic-pan-ebola/1000/v1.0.0/primer.bed
@@ -127,4 +127,4 @@ NC_006432.1	17045	17078	81307655_18_LEFT_1	1	+	GCCTTACTATTGATCCAGAAATACCAAGTTAAA
 NC_006432.1	17045	17078	81307655_18_LEFT_2	1	+	GCCTTACTATTGATTCAGAAATACCAAGTTAAG
 NC_006432.1	18096	18122	81307655_18_RIGHT_0	1	-	CCCTGTCAGCCTTTCAATAAGCTTAA
 NC_006432.1	18096	18122	81307655_18_RIGHT_1	1	-	CCCTGTCAGCCTTTCGATAAGCTTAA
-NC_006432.1	18096	18120	81307655_18_RIGHT_2	1	-	TGGTGAGCCGGTCCATAAGTTTTA
+NC_006432.1	18096	18120	81307655_18_RIGHT_2	1	-	TGGTGAGCCGGTCCATAAGTTTTA
diff --git a/primerschemes/artic-pan-ebola/1000/v1.0.0/reference.fasta b/primerschemes/artic-pan-ebola/1000/v1.0.0/reference.fasta
@@ -313,4 +313,4 @@ TATACAGCCAAAATATTTCATAGGGCCGATGGGAATAACATAAGAGGAACATGATCAATG
 AACCCTTTATTCCAACTAGGCAGTTGATTGATAATCTACAAATTCCATAAGATGTTCTTA
 CGATATTCTTTTGTTTTTAATCTCAATGTCAATGATTTAATAAGTAATAATAAAAAAATC
 ACATTAAAGATGCAGGAAGATCTTGACCTCGCCAGGAAAATTAAGCGCACACAAATAAAT
-TAAAAAATCTGTATTTTCTCTTTTTTGTGTGTCCA
+TAAAAAATCTGTATTTTCTCTTTTTTGTGTGTCCA
diff --git a/primerschemes/artic-sars-cov-2/400/v1.0.0/README.md b/primerschemes/artic-sars-cov-2/400/v1.0.0/README.md
@@ -1,5 +1,7 @@
 # artic-sars-cov-2 400bp v1.0.0
 
+[primalscheme labs](https://labs.primalscheme.com/detail/artic-sars-cov-2/400/v1.0.0)
+
 ## Description
 
 Schemes generated for the SARs-CoV-2 Outbreak
@@ -13,8 +15,8 @@ Schemes generated for the SARs-CoV-2 Outbreak
     "ampliconsize": 400,
     "schemeversion": "v1.0.0",
     "schemename": "artic-sars-cov-2",
-    "primer_bed_md5": "578f9cb933e01de0f3e9921cec14e5dc",
-    "reference_fasta_md5": "92ed86bf00cf94f9daef6acc81a8e48e",
+    "primer_bed_md5": "c79fcfba30e22def02857c8455576a82",
+    "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c",
     "status": "deprecated",
     "citations": [
         "https://doi.org/10.1038/nprot.2017.066"
@@ -29,16 +31,24 @@ Schemes generated for the SARs-CoV-2 Outbreak
     ],
     "license": "CC-BY-4.0",
     "primerclass": "primerschemes",
-    "infoschema": "v1.3.0",
-    "articbedversion": "v2.0",
-    "description": "Schemes generated for the SARs-CoV-2 Outbreak",
-    "derivedfrom": null,
+    "infoschema": "v2.0.0",
+    "articbedversion": "v3.0",
     "collections": [
-        "WHOLE-GENOME",
         "QUICK-LAB",
-        "ARTIC",
-        "WASTE-WATER"
-    ]
+        "WHOLE-GENOME",
+        "WASTE-WATER",
+        "ARTIC"
+    ],
+    "links": {
+        "protocals": [],
+        "validation": [],
+        "homepage": [],
+        "vendors": [],
+        "misc": []
+    },
+    "description": "Schemes generated for the SARs-CoV-2 Outbreak",
+    "derivedfrom": null,
+    "contactinfo": null
 }
 ```
 
diff --git a/primerschemes/artic-sars-cov-2/400/v1.0.0/info.json b/primerschemes/artic-sars-cov-2/400/v1.0.0/info.json
@@ -2,8 +2,8 @@
     "ampliconsize": 400,
     "schemeversion": "v1.0.0",
     "schemename": "artic-sars-cov-2",
-    "primer_bed_md5": "578f9cb933e01de0f3e9921cec14e5dc",
-    "reference_fasta_md5": "92ed86bf00cf94f9daef6acc81a8e48e",
+    "primer_bed_md5": "c79fcfba30e22def02857c8455576a82",
+    "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c",
     "status": "deprecated",
     "citations": [
         "https://doi.org/10.1038/nprot.2017.066"
@@ -18,14 +18,22 @@
     ],
     "license": "CC-BY-4.0",
     "primerclass": "primerschemes",
-    "infoschema": "v1.3.0",
-    "articbedversion": "v2.0",
-    "description": "Schemes generated for the SARs-CoV-2 Outbreak",
-    "derivedfrom": null,
+    "infoschema": "v2.0.0",
+    "articbedversion": "v3.0",
     "collections": [
-        "WHOLE-GENOME",
         "QUICK-LAB",
-        "ARTIC",
-        "WASTE-WATER"
-    ]
+        "WHOLE-GENOME",
+        "WASTE-WATER",
+        "ARTIC"
+    ],
+    "links": {
+        "protocals": [],
+        "validation": [],
+        "homepage": [],
+        "vendors": [],
+        "misc": []
+    },
+    "description": "Schemes generated for the SARs-CoV-2 Outbreak",
+    "derivedfrom": null,
+    "contactinfo": null
 }