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HIV-1 followup #194

Merged
merged 12 commits into from
May 6, 2024
Merged

HIV-1 followup #194

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d507f41
fix: path in readme
ivan-aksamentov May 6, 2024
6fc7d4f
fix: add attributes
ivan-aksamentov May 6, 2024
19463ea
feat: toggle "experimental" flag on
ivan-aksamentov May 6, 2024
29fdce6
chore: rebuild [skip ci]
nextstrain-bot May 6, 2024
9a28be5
feat: move `neherlab/hiv-1` to `neherlab/hiv-1/hxb2`
ivan-aksamentov May 6, 2024
e9cb401
feat: fix path in readme after moving
ivan-aksamentov May 6, 2024
ad37bd3
chore: rebuild [skip ci]
nextstrain-bot May 6, 2024
8f4e142
chore: remove old data output
ivan-aksamentov May 6, 2024
9b1955b
feat: add hiv-1 shortcut
ivan-aksamentov May 6, 2024
242e527
chore: rebuild [skip ci]
nextstrain-bot May 6, 2024
dc6b8b4
fix: set experimental attribute correctly
ivan-aksamentov May 6, 2024
8f0ecf0
chore: rebuild [skip ci]
nextstrain-bot May 6, 2024
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3 changes: 2 additions & 1 deletion data/community/collection.json
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Expand Up @@ -16,6 +16,7 @@
},
"dataset_order": [
"community/isuvdl/mazeller/prrsv2/orf5/yimim2023",
"community/neherlab/hiv-1"
"community/neherlab/hiv-1",
"community/neherlab/hiv-1/hxb2"
]
}
0 data/community/neherlab/hiv-1/CHANGELOG.md → ...ommunity/neherlab/hiv-1/hxb2/CHANGELOG.md
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2 changes: 1 addition & 1 deletion data/community/neherlab/hiv-1/README.md → data/community/neherlab/hiv-1/hxb2/README.md
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Expand Up @@ -5,7 +5,7 @@
| authors | [Richard Neher (U Basel)](https://neherlab.org), [Thomas Leitner (LANL)](https://public.lanl.gov/tkl/) |
| data source | LANL database and Genbank |
| workflow | [github.com/neherlab/HIV-nextclade](https://github.com/neherlab/HIV-nextclade) |
| nextclade dataset path | neherlab/HIV-1 |
| nextclade dataset path | community/neherlab/hiv-1/hxb2 |
| reference | [NC_001802](https://www.ncbi.nlm.nih.gov/nuccore/NC_001802) |

This Nextclade data set aligns sequences to the HXB2 reference and finds the closest match in a reference tree build from the [2021 Super filtered Alignment](https://www.hiv.lanl.gov/content/sequence/NEWALIGN/help.html#filter) provided by LANL.
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0 ...ity/neherlab/hiv-1/genome_annotation.gff3 → ...eherlab/hiv-1/hxb2/genome_annotation.gff3
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15 changes: 12 additions & 3 deletions data/community/neherlab/hiv-1/pathogen.json → ...mmunity/neherlab/hiv-1/hxb2/pathogen.json
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Expand Up @@ -25,7 +25,7 @@
],
"deprecated": false,
"enabled": true,
"experimental": false,
"experimental": true,
"files": {
"pathogenJson": "pathogen.json",
"changelog": "CHANGELOG.md",
Expand Down Expand Up @@ -66,5 +66,14 @@
"scoreWeight": 40
}
},
"schemaVersion": "3.0.0"
}
"schemaVersion": "3.0.0",
"attributes": {
"name": "HIV-1 (HXB2)",
"reference accession": "NC_001802",
"reference name": "HIV-1, strain HXB2",
"experimental": true
},
"shortcuts": [
"neherlab/hiv-1"
]
}
0 .../community/neherlab/hiv-1/reference.fasta → ...unity/neherlab/hiv-1/hxb2/reference.fasta
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0 .../community/neherlab/hiv-1/sequences.fasta → ...unity/neherlab/hiv-1/hxb2/sequences.fasta
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0 data/community/neherlab/hiv-1/tree.json → data/community/neherlab/hiv-1/hxb2/tree.json
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0 ...ty/neherlab/hiv-1/unreleased/CHANGELOG.md → ...herlab/hiv-1/hxb2/unreleased/CHANGELOG.md
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2 changes: 1 addition & 1 deletion ...unity/neherlab/hiv-1/unreleased/README.md → .../neherlab/hiv-1/hxb2/unreleased/README.md
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Expand Up @@ -5,7 +5,7 @@
| authors | [Richard Neher (U Basel)](https://neherlab.org), [Thomas Leitner (LANL)](https://public.lanl.gov/tkl/) |
| data source | LANL database and Genbank |
| workflow | [github.com/neherlab/HIV-nextclade](https://github.com/neherlab/HIV-nextclade) |
| nextclade dataset path | neherlab/HIV-1 |
| nextclade dataset path | community/neherlab/hiv-1/hxb2 |
| reference | [NC_001802](https://www.ncbi.nlm.nih.gov/nuccore/NC_001802) |

This Nextclade data set aligns sequences to the HXB2 reference and finds the closest match in a reference tree build from the [2021 Super filtered Alignment](https://www.hiv.lanl.gov/content/sequence/NEWALIGN/help.html#filter) provided by LANL.
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Binary file renamed ...ity/neherlab/hiv-1/unreleased/dataset.zip → ...eherlab/hiv-1/hxb2/unreleased/dataset.zip
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0 ...b/hiv-1/unreleased/genome_annotation.gff3 → ...-1/hxb2/unreleased/genome_annotation.gff3
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11 changes: 10 additions & 1 deletion ...y/neherlab/hiv-1/unreleased/pathogen.json → ...erlab/hiv-1/hxb2/unreleased/pathogen.json
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Expand Up @@ -40,7 +40,7 @@
],
"deprecated": false,
"enabled": true,
"experimental": false,
"experimental": true,
"files": {
"pathogenJson": "pathogen.json",
"changelog": "CHANGELOG.md",
Expand Down Expand Up @@ -85,6 +85,15 @@
}
},
"schemaVersion": "3.0.0",
"attributes": {
"name": "HIV-1 (HXB2)",
"reference accession": "NC_001802",
"reference name": "HIV-1, strain HXB2",
"experimental": true
},
"shortcuts": [
"neherlab/hiv-1"
],
"version": {
"tag": "unreleased",
"compatibility": {
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0 ...neherlab/hiv-1/unreleased/reference.fasta → ...lab/hiv-1/hxb2/unreleased/reference.fasta
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0 ...neherlab/hiv-1/unreleased/sequences.fasta → ...lab/hiv-1/hxb2/unreleased/sequences.fasta
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0 ...unity/neherlab/hiv-1/unreleased/tree.json → .../neherlab/hiv-1/hxb2/unreleased/tree.json
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11 changes: 10 additions & 1 deletion data_output/index.json
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Expand Up @@ -2432,8 +2432,17 @@
}
},
{
"path": "community/neherlab/hiv-1",
"path": "community/neherlab/hiv-1/hxb2",
"shortcuts": [
"neherlab/hiv-1"
],
"enabled": true,
"attributes": {
"name": "HIV-1 (HXB2)",
"reference accession": "NC_001802",
"reference name": "HIV-1, strain HXB2",
"experimental": true
},
"files": {
"pathogenJson": "pathogen.json",
"changelog": "CHANGELOG.md",
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2 changes: 1 addition & 1 deletion data_output/minimizer_index.json
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Expand Up @@ -85835,7 +85835,7 @@
"nMinimizers": 44
},
{
"name": "community/neherlab/hiv-1",
"name": "community/neherlab/hiv-1/hxb2",
"length": 9181,
"nMinimizers": 544
},
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