diff --git a/data/nextstrain/sars-cov-2/BA.2.86/CHANGELOG.md b/data/nextstrain/sars-cov-2/BA.2.86/CHANGELOG.md index ce46019f..6e7abf4b 100644 --- a/data/nextstrain/sars-cov-2/BA.2.86/CHANGELOG.md +++ b/data/nextstrain/sars-cov-2/BA.2.86/CHANGELOG.md @@ -1,4 +1,4 @@ -## Unreleased +## 2024-04-25T01:03:07Z - fix: Increase Nextclade alignment parameter "excessBandwidth" from 9 to 12 to correctly align complex series of indels that has arisen in Spike NTD with the occurrence of S:31- in some JN.1. The bandwidth is chosen to be as small as possible (to ensure fast runtime) but as large as necessary for correct alignment. As a result, occasional adjustments like here are required. Nothing else is changed in this SARS-CoV-2 dataset update. diff --git a/data/nextstrain/sars-cov-2/BA.2/CHANGELOG.md b/data/nextstrain/sars-cov-2/BA.2/CHANGELOG.md index 9a35077d..6b37d072 100644 --- a/data/nextstrain/sars-cov-2/BA.2/CHANGELOG.md +++ b/data/nextstrain/sars-cov-2/BA.2/CHANGELOG.md @@ -1,4 +1,4 @@ -## Unreleased +## 2024-04-25T01:03:07Z - fix: Increase Nextclade alignment parameter "excessBandwidth" from 9 to 12 to correctly align complex series of indels that has arisen in Spike NTD with the occurrence of S:31- in some JN.1. The bandwidth is chosen to be as small as possible (to ensure fast runtime) but as large as necessary for correct alignment. As a result, occasional adjustments like here are required. Nothing else is changed in this SARS-CoV-2 dataset update. diff --git a/data/nextstrain/sars-cov-2/XBB/CHANGELOG.md b/data/nextstrain/sars-cov-2/XBB/CHANGELOG.md index ce46019f..6e7abf4b 100644 --- a/data/nextstrain/sars-cov-2/XBB/CHANGELOG.md +++ b/data/nextstrain/sars-cov-2/XBB/CHANGELOG.md @@ -1,4 +1,4 @@ -## Unreleased +## 2024-04-25T01:03:07Z - fix: Increase Nextclade alignment parameter "excessBandwidth" from 9 to 12 to correctly align complex series of indels that has arisen in Spike NTD with the occurrence of S:31- in some JN.1. The bandwidth is chosen to be as small as possible (to ensure fast runtime) but as large as necessary for correct alignment. As a result, occasional adjustments like here are required. Nothing else is changed in this SARS-CoV-2 dataset update. diff --git a/data/nextstrain/sars-cov-2/wuhan-hu-1/orfs/CHANGELOG.md b/data/nextstrain/sars-cov-2/wuhan-hu-1/orfs/CHANGELOG.md index 14c5b291..8fedea46 100644 --- a/data/nextstrain/sars-cov-2/wuhan-hu-1/orfs/CHANGELOG.md +++ b/data/nextstrain/sars-cov-2/wuhan-hu-1/orfs/CHANGELOG.md @@ -1,4 +1,4 @@ -## Unreleased +## 2024-04-25T01:03:07Z - fix: Increase Nextclade alignment parameter "excessBandwidth" from 9 to 12 to correctly align complex series of indels that has arisen in Spike NTD with the occurrence of S:31- in some JN.1. The bandwidth is chosen to be as small as possible (to ensure fast runtime) but as large as necessary for correct alignment. As a result, occasional adjustments like here are required. Nothing else is changed in this SARS-CoV-2 dataset update. diff --git a/data/nextstrain/sars-cov-2/wuhan-hu-1/proteins/CHANGELOG.md b/data/nextstrain/sars-cov-2/wuhan-hu-1/proteins/CHANGELOG.md index 04f30ffd..9473f47e 100644 --- a/data/nextstrain/sars-cov-2/wuhan-hu-1/proteins/CHANGELOG.md +++ b/data/nextstrain/sars-cov-2/wuhan-hu-1/proteins/CHANGELOG.md @@ -1,4 +1,4 @@ -## Unreleased +## 2024-04-25T01:03:07Z - fix: Increase Nextclade alignment parameter "excessBandwidth" from 9 to 12 to correctly align complex series of indels that has arisen in Spike NTD with the occurrence of S:31- in some JN.1. The bandwidth is chosen to be as small as possible (to ensure fast runtime) but as large as necessary for correct alignment. As a result, occasional adjustments like here are required. Nothing else is changed in this SARS-CoV-2 dataset update. diff --git a/data_output/index.json b/data_output/index.json index 054369c3..50da1d38 100644 --- a/data_output/index.json +++ b/data_output/index.json @@ -85,7 +85,8 @@ }, "versions": [ { - "tag": "unreleased", + "updatedAt": "2024-04-25T01:03:07Z", + "tag": "2024-04-25--01-03-07Z", "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" @@ -117,7 +118,8 @@ } ], "version": { - "tag": "unreleased", + "updatedAt": "2024-04-25T01:03:07Z", + "tag": "2024-04-25--01-03-07Z", "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" @@ -180,7 +182,8 @@ }, "versions": [ { - "tag": "unreleased", + "updatedAt": "2024-04-25T01:03:07Z", + "tag": "2024-04-25--01-03-07Z", "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" @@ -212,7 +215,8 @@ } ], "version": { - "tag": "unreleased", + "updatedAt": "2024-04-25T01:03:07Z", + "tag": "2024-04-25--01-03-07Z", "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" @@ -278,7 +282,8 @@ }, "versions": [ { - "tag": "unreleased", + "updatedAt": "2024-04-25T01:03:07Z", + "tag": "2024-04-25--01-03-07Z", "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" @@ -310,7 +315,8 @@ } ], "version": { - "tag": "unreleased", + "updatedAt": "2024-04-25T01:03:07Z", + "tag": "2024-04-25--01-03-07Z", "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" @@ -373,7 +379,8 @@ }, "versions": [ { - "tag": "unreleased", + "updatedAt": "2024-04-25T01:03:07Z", + "tag": "2024-04-25--01-03-07Z", "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" @@ -405,7 +412,8 @@ } ], "version": { - "tag": "unreleased", + "updatedAt": "2024-04-25T01:03:07Z", + "tag": "2024-04-25--01-03-07Z", "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" @@ -468,7 +476,8 @@ }, "versions": [ { - "tag": "unreleased", + "updatedAt": "2024-04-25T01:03:07Z", + "tag": "2024-04-25--01-03-07Z", "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" @@ -500,7 +509,8 @@ } ], "version": { - "tag": "unreleased", + "updatedAt": "2024-04-25T01:03:07Z", + "tag": "2024-04-25--01-03-07Z", "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" diff --git a/data_output/nextstrain/sars-cov-2/BA.2.86/unreleased/CHANGELOG.md b/data_output/nextstrain/sars-cov-2/BA.2.86/2024-04-25--01-03-07Z/CHANGELOG.md similarity index 99% rename from data_output/nextstrain/sars-cov-2/BA.2.86/unreleased/CHANGELOG.md rename to data_output/nextstrain/sars-cov-2/BA.2.86/2024-04-25--01-03-07Z/CHANGELOG.md index ce46019f..6e7abf4b 100644 --- a/data_output/nextstrain/sars-cov-2/BA.2.86/unreleased/CHANGELOG.md +++ b/data_output/nextstrain/sars-cov-2/BA.2.86/2024-04-25--01-03-07Z/CHANGELOG.md @@ -1,4 +1,4 @@ -## Unreleased +## 2024-04-25T01:03:07Z - fix: Increase Nextclade alignment parameter "excessBandwidth" from 9 to 12 to correctly align complex series of indels that has arisen in Spike NTD with the occurrence of S:31- in some JN.1. The bandwidth is chosen to be as small as possible (to ensure fast runtime) but as large as necessary for correct alignment. As a result, occasional adjustments like here are required. Nothing else is changed in this SARS-CoV-2 dataset update. diff --git a/data_output/nextstrain/sars-cov-2/BA.2.86/unreleased/README.md b/data_output/nextstrain/sars-cov-2/BA.2.86/2024-04-25--01-03-07Z/README.md similarity index 100% rename from data_output/nextstrain/sars-cov-2/BA.2.86/unreleased/README.md rename to data_output/nextstrain/sars-cov-2/BA.2.86/2024-04-25--01-03-07Z/README.md diff --git a/data_output/nextstrain/sars-cov-2/BA.2.86/unreleased/dataset.zip b/data_output/nextstrain/sars-cov-2/BA.2.86/2024-04-25--01-03-07Z/dataset.zip similarity index 99% rename from data_output/nextstrain/sars-cov-2/BA.2.86/unreleased/dataset.zip rename to data_output/nextstrain/sars-cov-2/BA.2.86/2024-04-25--01-03-07Z/dataset.zip index eeccbb3a..2b8987e4 100644 Binary files a/data_output/nextstrain/sars-cov-2/BA.2.86/unreleased/dataset.zip and b/data_output/nextstrain/sars-cov-2/BA.2.86/2024-04-25--01-03-07Z/dataset.zip differ diff --git a/data_output/nextstrain/sars-cov-2/BA.2.86/unreleased/genome_annotation.gff3 b/data_output/nextstrain/sars-cov-2/BA.2.86/2024-04-25--01-03-07Z/genome_annotation.gff3 similarity index 100% rename from data_output/nextstrain/sars-cov-2/BA.2.86/unreleased/genome_annotation.gff3 rename to data_output/nextstrain/sars-cov-2/BA.2.86/2024-04-25--01-03-07Z/genome_annotation.gff3 diff --git a/data_output/nextstrain/sars-cov-2/BA.2.86/unreleased/pathogen.json b/data_output/nextstrain/sars-cov-2/BA.2.86/2024-04-25--01-03-07Z/pathogen.json similarity index 99% rename from data_output/nextstrain/sars-cov-2/BA.2.86/unreleased/pathogen.json rename to data_output/nextstrain/sars-cov-2/BA.2.86/2024-04-25--01-03-07Z/pathogen.json index 98e841db..4c24a34d 100644 --- a/data_output/nextstrain/sars-cov-2/BA.2.86/unreleased/pathogen.json +++ b/data_output/nextstrain/sars-cov-2/BA.2.86/2024-04-25--01-03-07Z/pathogen.json @@ -2690,7 +2690,8 @@ }, "schemaVersion": "3.0.0", "version": { - "tag": "unreleased", + "updatedAt": "2024-04-25T01:03:07Z", + "tag": "2024-04-25--01-03-07Z", "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" diff --git a/data_output/nextstrain/sars-cov-2/BA.2.86/unreleased/reference.fasta b/data_output/nextstrain/sars-cov-2/BA.2.86/2024-04-25--01-03-07Z/reference.fasta similarity index 100% rename from data_output/nextstrain/sars-cov-2/BA.2.86/unreleased/reference.fasta rename to data_output/nextstrain/sars-cov-2/BA.2.86/2024-04-25--01-03-07Z/reference.fasta diff --git a/data_output/nextstrain/sars-cov-2/BA.2.86/unreleased/sequences.fasta b/data_output/nextstrain/sars-cov-2/BA.2.86/2024-04-25--01-03-07Z/sequences.fasta similarity index 100% rename from data_output/nextstrain/sars-cov-2/BA.2.86/unreleased/sequences.fasta rename to data_output/nextstrain/sars-cov-2/BA.2.86/2024-04-25--01-03-07Z/sequences.fasta diff --git a/data_output/nextstrain/sars-cov-2/BA.2.86/unreleased/tree.json b/data_output/nextstrain/sars-cov-2/BA.2.86/2024-04-25--01-03-07Z/tree.json similarity index 100% rename from data_output/nextstrain/sars-cov-2/BA.2.86/unreleased/tree.json rename to data_output/nextstrain/sars-cov-2/BA.2.86/2024-04-25--01-03-07Z/tree.json diff --git a/data_output/nextstrain/sars-cov-2/BA.2/unreleased/CHANGELOG.md b/data_output/nextstrain/sars-cov-2/BA.2/2024-04-25--01-03-07Z/CHANGELOG.md similarity index 99% rename from data_output/nextstrain/sars-cov-2/BA.2/unreleased/CHANGELOG.md rename to data_output/nextstrain/sars-cov-2/BA.2/2024-04-25--01-03-07Z/CHANGELOG.md index 9a35077d..6b37d072 100644 --- a/data_output/nextstrain/sars-cov-2/BA.2/unreleased/CHANGELOG.md +++ b/data_output/nextstrain/sars-cov-2/BA.2/2024-04-25--01-03-07Z/CHANGELOG.md @@ -1,4 +1,4 @@ -## Unreleased +## 2024-04-25T01:03:07Z - fix: Increase Nextclade alignment parameter "excessBandwidth" from 9 to 12 to correctly align complex series of indels that has arisen in Spike NTD with the occurrence of S:31- in some JN.1. The bandwidth is chosen to be as small as possible (to ensure fast runtime) but as large as necessary for correct alignment. As a result, occasional adjustments like here are required. Nothing else is changed in this SARS-CoV-2 dataset update. diff --git a/data_output/nextstrain/sars-cov-2/BA.2/unreleased/README.md b/data_output/nextstrain/sars-cov-2/BA.2/2024-04-25--01-03-07Z/README.md similarity index 100% rename from data_output/nextstrain/sars-cov-2/BA.2/unreleased/README.md rename to data_output/nextstrain/sars-cov-2/BA.2/2024-04-25--01-03-07Z/README.md diff --git a/data_output/nextstrain/sars-cov-2/BA.2/unreleased/dataset.zip b/data_output/nextstrain/sars-cov-2/BA.2/2024-04-25--01-03-07Z/dataset.zip similarity index 99% rename from data_output/nextstrain/sars-cov-2/BA.2/unreleased/dataset.zip rename to data_output/nextstrain/sars-cov-2/BA.2/2024-04-25--01-03-07Z/dataset.zip index 3fc4216f..7e682f72 100644 Binary files a/data_output/nextstrain/sars-cov-2/BA.2/unreleased/dataset.zip and b/data_output/nextstrain/sars-cov-2/BA.2/2024-04-25--01-03-07Z/dataset.zip differ diff --git a/data_output/nextstrain/sars-cov-2/BA.2/unreleased/genome_annotation.gff3 b/data_output/nextstrain/sars-cov-2/BA.2/2024-04-25--01-03-07Z/genome_annotation.gff3 similarity index 100% rename from data_output/nextstrain/sars-cov-2/BA.2/unreleased/genome_annotation.gff3 rename to data_output/nextstrain/sars-cov-2/BA.2/2024-04-25--01-03-07Z/genome_annotation.gff3 diff --git a/data_output/nextstrain/sars-cov-2/BA.2/unreleased/pathogen.json b/data_output/nextstrain/sars-cov-2/BA.2/2024-04-25--01-03-07Z/pathogen.json similarity index 99% rename from data_output/nextstrain/sars-cov-2/BA.2/unreleased/pathogen.json rename to data_output/nextstrain/sars-cov-2/BA.2/2024-04-25--01-03-07Z/pathogen.json index be521ec5..2ec243b9 100644 --- a/data_output/nextstrain/sars-cov-2/BA.2/unreleased/pathogen.json +++ b/data_output/nextstrain/sars-cov-2/BA.2/2024-04-25--01-03-07Z/pathogen.json @@ -2690,7 +2690,8 @@ }, "schemaVersion": "3.0.0", "version": { - "tag": "unreleased", + "updatedAt": "2024-04-25T01:03:07Z", + "tag": "2024-04-25--01-03-07Z", "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" diff --git a/data_output/nextstrain/sars-cov-2/BA.2/unreleased/reference.fasta b/data_output/nextstrain/sars-cov-2/BA.2/2024-04-25--01-03-07Z/reference.fasta similarity index 100% rename from data_output/nextstrain/sars-cov-2/BA.2/unreleased/reference.fasta rename to data_output/nextstrain/sars-cov-2/BA.2/2024-04-25--01-03-07Z/reference.fasta diff --git a/data_output/nextstrain/sars-cov-2/BA.2/unreleased/sequences.fasta b/data_output/nextstrain/sars-cov-2/BA.2/2024-04-25--01-03-07Z/sequences.fasta similarity index 100% rename from data_output/nextstrain/sars-cov-2/BA.2/unreleased/sequences.fasta rename to data_output/nextstrain/sars-cov-2/BA.2/2024-04-25--01-03-07Z/sequences.fasta diff --git a/data_output/nextstrain/sars-cov-2/BA.2/unreleased/tree.json b/data_output/nextstrain/sars-cov-2/BA.2/2024-04-25--01-03-07Z/tree.json similarity index 100% rename from data_output/nextstrain/sars-cov-2/BA.2/unreleased/tree.json rename to data_output/nextstrain/sars-cov-2/BA.2/2024-04-25--01-03-07Z/tree.json diff --git a/data_output/nextstrain/sars-cov-2/XBB/unreleased/CHANGELOG.md b/data_output/nextstrain/sars-cov-2/XBB/2024-04-25--01-03-07Z/CHANGELOG.md similarity index 99% rename from data_output/nextstrain/sars-cov-2/XBB/unreleased/CHANGELOG.md rename to data_output/nextstrain/sars-cov-2/XBB/2024-04-25--01-03-07Z/CHANGELOG.md index ce46019f..6e7abf4b 100644 --- a/data_output/nextstrain/sars-cov-2/XBB/unreleased/CHANGELOG.md +++ b/data_output/nextstrain/sars-cov-2/XBB/2024-04-25--01-03-07Z/CHANGELOG.md @@ -1,4 +1,4 @@ -## Unreleased +## 2024-04-25T01:03:07Z - fix: Increase Nextclade alignment parameter "excessBandwidth" from 9 to 12 to correctly align complex series of indels that has arisen in Spike NTD with the occurrence of S:31- in some JN.1. The bandwidth is chosen to be as small as possible (to ensure fast runtime) but as large as necessary for correct alignment. As a result, occasional adjustments like here are required. Nothing else is changed in this SARS-CoV-2 dataset update. diff --git a/data_output/nextstrain/sars-cov-2/XBB/unreleased/README.md b/data_output/nextstrain/sars-cov-2/XBB/2024-04-25--01-03-07Z/README.md similarity index 100% rename from data_output/nextstrain/sars-cov-2/XBB/unreleased/README.md rename to data_output/nextstrain/sars-cov-2/XBB/2024-04-25--01-03-07Z/README.md diff --git a/data_output/nextstrain/sars-cov-2/XBB/unreleased/dataset.zip b/data_output/nextstrain/sars-cov-2/XBB/2024-04-25--01-03-07Z/dataset.zip similarity index 99% rename from data_output/nextstrain/sars-cov-2/XBB/unreleased/dataset.zip rename to data_output/nextstrain/sars-cov-2/XBB/2024-04-25--01-03-07Z/dataset.zip index e4a6df42..68a4fb90 100644 Binary files a/data_output/nextstrain/sars-cov-2/XBB/unreleased/dataset.zip and b/data_output/nextstrain/sars-cov-2/XBB/2024-04-25--01-03-07Z/dataset.zip differ diff --git a/data_output/nextstrain/sars-cov-2/XBB/unreleased/genome_annotation.gff3 b/data_output/nextstrain/sars-cov-2/XBB/2024-04-25--01-03-07Z/genome_annotation.gff3 similarity index 100% rename from data_output/nextstrain/sars-cov-2/XBB/unreleased/genome_annotation.gff3 rename to data_output/nextstrain/sars-cov-2/XBB/2024-04-25--01-03-07Z/genome_annotation.gff3 diff --git a/data_output/nextstrain/sars-cov-2/XBB/unreleased/pathogen.json b/data_output/nextstrain/sars-cov-2/XBB/2024-04-25--01-03-07Z/pathogen.json similarity index 99% rename from data_output/nextstrain/sars-cov-2/XBB/unreleased/pathogen.json rename to data_output/nextstrain/sars-cov-2/XBB/2024-04-25--01-03-07Z/pathogen.json index b9d1e810..fbd5e3fb 100644 --- a/data_output/nextstrain/sars-cov-2/XBB/unreleased/pathogen.json +++ b/data_output/nextstrain/sars-cov-2/XBB/2024-04-25--01-03-07Z/pathogen.json @@ -2690,7 +2690,8 @@ }, "schemaVersion": "3.0.0", "version": { - "tag": "unreleased", + "updatedAt": "2024-04-25T01:03:07Z", + "tag": "2024-04-25--01-03-07Z", "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" diff --git a/data_output/nextstrain/sars-cov-2/XBB/unreleased/reference.fasta b/data_output/nextstrain/sars-cov-2/XBB/2024-04-25--01-03-07Z/reference.fasta similarity index 100% rename from data_output/nextstrain/sars-cov-2/XBB/unreleased/reference.fasta rename to data_output/nextstrain/sars-cov-2/XBB/2024-04-25--01-03-07Z/reference.fasta diff --git a/data_output/nextstrain/sars-cov-2/XBB/unreleased/sequences.fasta b/data_output/nextstrain/sars-cov-2/XBB/2024-04-25--01-03-07Z/sequences.fasta similarity index 100% rename from data_output/nextstrain/sars-cov-2/XBB/unreleased/sequences.fasta rename to data_output/nextstrain/sars-cov-2/XBB/2024-04-25--01-03-07Z/sequences.fasta diff --git a/data_output/nextstrain/sars-cov-2/XBB/unreleased/tree.json b/data_output/nextstrain/sars-cov-2/XBB/2024-04-25--01-03-07Z/tree.json similarity index 100% rename from data_output/nextstrain/sars-cov-2/XBB/unreleased/tree.json rename to data_output/nextstrain/sars-cov-2/XBB/2024-04-25--01-03-07Z/tree.json diff --git a/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/CHANGELOG.md b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/2024-04-25--01-03-07Z/CHANGELOG.md similarity index 99% rename from data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/CHANGELOG.md rename to data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/2024-04-25--01-03-07Z/CHANGELOG.md index 14c5b291..8fedea46 100644 --- a/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/CHANGELOG.md +++ b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/2024-04-25--01-03-07Z/CHANGELOG.md @@ -1,4 +1,4 @@ -## Unreleased +## 2024-04-25T01:03:07Z - fix: Increase Nextclade alignment parameter "excessBandwidth" from 9 to 12 to correctly align complex series of indels that has arisen in Spike NTD with the occurrence of S:31- in some JN.1. The bandwidth is chosen to be as small as possible (to ensure fast runtime) but as large as necessary for correct alignment. As a result, occasional adjustments like here are required. Nothing else is changed in this SARS-CoV-2 dataset update. diff --git a/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/README.md b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/2024-04-25--01-03-07Z/README.md similarity index 100% rename from data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/README.md rename to data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/2024-04-25--01-03-07Z/README.md diff --git a/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/dataset.zip b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/2024-04-25--01-03-07Z/dataset.zip similarity index 99% rename from data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/dataset.zip rename to data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/2024-04-25--01-03-07Z/dataset.zip index 38bdc7b2..8317494f 100644 Binary files a/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/dataset.zip and b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/2024-04-25--01-03-07Z/dataset.zip differ diff --git a/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/genome_annotation.gff3 b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/2024-04-25--01-03-07Z/genome_annotation.gff3 similarity index 100% rename from data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/genome_annotation.gff3 rename to data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/2024-04-25--01-03-07Z/genome_annotation.gff3 diff --git a/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/pathogen.json b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/2024-04-25--01-03-07Z/pathogen.json similarity index 99% rename from data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/pathogen.json rename to data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/2024-04-25--01-03-07Z/pathogen.json index 25318fb4..e2e56bc5 100644 --- a/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/pathogen.json +++ b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/2024-04-25--01-03-07Z/pathogen.json @@ -2690,7 +2690,8 @@ }, "schemaVersion": "3.0.0", "version": { - "tag": "unreleased", + "updatedAt": "2024-04-25T01:03:07Z", + "tag": "2024-04-25--01-03-07Z", "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" diff --git a/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/reference.fasta b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/2024-04-25--01-03-07Z/reference.fasta similarity index 100% rename from data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/reference.fasta rename to data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/2024-04-25--01-03-07Z/reference.fasta diff --git a/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/sequences.fasta b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/2024-04-25--01-03-07Z/sequences.fasta similarity index 100% rename from data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/sequences.fasta rename to data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/2024-04-25--01-03-07Z/sequences.fasta diff --git a/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/tree.json b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/2024-04-25--01-03-07Z/tree.json similarity index 100% rename from data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/tree.json rename to data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/2024-04-25--01-03-07Z/tree.json diff --git a/data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/unreleased/CHANGELOG.md b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/2024-04-25--01-03-07Z/CHANGELOG.md similarity index 99% rename from data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/unreleased/CHANGELOG.md rename to data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/2024-04-25--01-03-07Z/CHANGELOG.md index 04f30ffd..9473f47e 100644 --- a/data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/unreleased/CHANGELOG.md +++ b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/2024-04-25--01-03-07Z/CHANGELOG.md @@ -1,4 +1,4 @@ -## Unreleased +## 2024-04-25T01:03:07Z - fix: Increase Nextclade alignment parameter "excessBandwidth" from 9 to 12 to correctly align complex series of indels that has arisen in Spike NTD with the occurrence of S:31- in some JN.1. The bandwidth is chosen to be as small as possible (to ensure fast runtime) but as large as necessary for correct alignment. As a result, occasional adjustments like here are required. Nothing else is changed in this SARS-CoV-2 dataset update. diff --git a/data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/unreleased/README.md b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/2024-04-25--01-03-07Z/README.md similarity index 100% rename from data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/unreleased/README.md rename to data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/2024-04-25--01-03-07Z/README.md diff --git a/data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/unreleased/dataset.zip b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/2024-04-25--01-03-07Z/dataset.zip similarity index 99% rename from data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/unreleased/dataset.zip rename to data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/2024-04-25--01-03-07Z/dataset.zip index fd85303f..53def08d 100644 Binary files a/data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/unreleased/dataset.zip and b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/2024-04-25--01-03-07Z/dataset.zip differ diff --git a/data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/unreleased/genome_annotation.gff3 b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/2024-04-25--01-03-07Z/genome_annotation.gff3 similarity index 100% rename from data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/unreleased/genome_annotation.gff3 rename to data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/2024-04-25--01-03-07Z/genome_annotation.gff3 diff --git a/data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/unreleased/pathogen.json b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/2024-04-25--01-03-07Z/pathogen.json similarity index 99% rename from data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/unreleased/pathogen.json rename to data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/2024-04-25--01-03-07Z/pathogen.json index d713279a..038a3147 100644 --- a/data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/unreleased/pathogen.json +++ b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/2024-04-25--01-03-07Z/pathogen.json @@ -2690,7 +2690,8 @@ }, "schemaVersion": "3.0.0", "version": { - "tag": "unreleased", + "updatedAt": "2024-04-25T01:03:07Z", + "tag": "2024-04-25--01-03-07Z", "compatibility": { "cli": "3.0.0-alpha.0", "web": "3.0.0-alpha.0" diff --git a/data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/unreleased/reference.fasta b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/2024-04-25--01-03-07Z/reference.fasta similarity index 100% rename from data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/unreleased/reference.fasta rename to data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/2024-04-25--01-03-07Z/reference.fasta diff --git a/data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/unreleased/sequences.fasta b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/2024-04-25--01-03-07Z/sequences.fasta similarity index 100% rename from data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/unreleased/sequences.fasta rename to data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/2024-04-25--01-03-07Z/sequences.fasta diff --git a/data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/unreleased/tree.json b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/2024-04-25--01-03-07Z/tree.json similarity index 100% rename from data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/unreleased/tree.json rename to data_output/nextstrain/sars-cov-2/wuhan-hu-1/proteins/2024-04-25--01-03-07Z/tree.json