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GitHub / bgruening / nextclade

Viral genome alignment, clade assignment, mutation calling, and quality checks

JSON API: https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bgruening%2Fnextclade

Fork of nextstrain/nextclade
Stars: 0
Forks: 0
Open Issues: 3

License: mit
Language: TypeScript
Repo Size: 52.1 MB
Dependencies: 2,896

Created: about 3 years ago
Updated: 29 days ago
Last pushed: 29 days ago
Last synced: 29 days ago

Files

Readme

Dependencies

docs/environment.yml pypi

.github/workflows/builder-docker-image.yml actions

actions/cache v3 composite
actions/checkout v3 composite
docker/login-action v2 composite

.github/workflows/cli.yml actions

actions/cache v3 composite
actions/checkout v3 composite
actions/download-artifact v3 composite
actions/upload-artifact v3 composite
docker/login-action v2 composite

.github/workflows/web.yml actions

actions/cache v3 composite
actions/checkout v3 composite
actions/download-artifact v3 composite
actions/upload-artifact v3 composite
docker/login-action v2 composite

packages_rs/nextclade-web/package.json npm

@babel/core 7.17.9 development
@babel/node 7.16.8 development
@babel/plugin-proposal-decorators 7.17.9 development
@babel/preset-env 7.16.11 development
@babel/preset-typescript 7.16.7 development
@mdx-js/loader 1.6.22 development
@mdx-js/react 1.6.22 development
@next/eslint-plugin-next 12.1.5 development
@next/mdx 12.1.5 development
@nuxt/friendly-errors-webpack-plugin 2.5.2 development
@primer/css 19.8.2 development
@schemastore/package 0.0.6 development
@svgr/webpack 6.2.1 development
@testing-library/jest-dom 5.16.4 development
@testing-library/react 13.1.1 development
@testing-library/user-event 14.1.1 development
@types/classnames 2.3.0 development
@types/compare-versions 3.3.0 development
@types/compression-webpack-plugin 9.0.0 development
@types/connect-history-api-fallback 1.3.5 development
@types/copy-webpack-plugin 6.4.3 development
@types/express 4.17.13 development
@types/extra-watch-webpack-plugin 1.0.3 development
@types/file-saver 2.0.5 development
@types/friendly-errors-webpack-plugin 0.1.4 development
@types/fs-extra 9.0.13 development
@types/glob 7.2.0 development
@types/history 4.7.11 development
@types/intercept-stdout 0.1.0 development
@types/jest 27.4.1 development
@types/jest-axe 3.5.3 development
@types/js-yaml 4.0.5 development
@types/jszip 3.4.1 development
@types/lodash 4.14.182 development
@types/lodash-webpack-plugin 0.11.6 development
@types/luxon 2.3.1 development
@types/mdx-js__react 1.5.5 development
@types/papaparse 5.3.2 development
@types/react 18.0.8 development
@types/react-copy-to-clipboard 5.0.4 development
@types/react-dom 18.0.2 development
@types/react-helmet 6.1.5 development
@types/react-no-ssr 1.1.3 development
@types/react-redux 7.1.24 development
@types/react-resize-detector 5.0.0 development
@types/react-router 5.1.18 development
@types/react-router-dom 5.3.3 development
@types/react-select 5.0.0 development
@types/react-toggle 4.0.3 development
@types/react-virtualized-auto-sizer 1.0.1 development
@types/react-window 1.8.5 development
@types/reactstrap 8.7.1 development
@types/recharts 1.8.23 development
@types/rimraf 3.0.2 development
@types/semver 7.3.9 development
@types/serialize-javascript 5.0.2 development
@types/styled-components 5.1.25 development
@types/terser-webpack-plugin 4.1.0 development
@types/url-join 4.0.1 development
@types/uuid 8.3.4 development
@types/webpack 5.28.0 development
@types/webpackbar 4.0.3 development
@typescript-eslint/eslint-plugin 5.21.0 development
@typescript-eslint/parser 5.21.0 development
@typescript-eslint/typescript-estree 5.21.0 development
all-contributors-cli 6.20.0 development
allow-methods 3.1.0 development
babel-plugin-parameter-decorator 1.0.16 development
babel-plugin-transform-typescript-metadata 0.3.2 development
compression-webpack-plugin 9.2.0 development
connect-history-api-fallback 1.6.0 development
conventional-changelog-cli 2.2.2 development
copy-webpack-plugin 10.2.4 development
cross-env 7.0.3 development
css-loader 6.7.1 development
dotenv 16.0.0 development
eslint 8.14.0 development
eslint-config-airbnb 19.0.4 development
eslint-config-airbnb-base 15.0.0 development
eslint-config-airbnb-typescript 17.0.0 development
eslint-config-next 12.1.5 development
eslint-config-prettier 8.5.0 development
eslint-config-react-app 7.0.1 development
eslint-formatter-codeframe 7.32.1 development
eslint-import-resolver-ts 0.4.2 development
eslint-import-resolver-typescript 2.7.1 development
eslint-loader 4.0.2 development
eslint-plugin-array-func 3.1.7 development
eslint-plugin-cflint 1.0.0 development
eslint-plugin-cypress 2.12.1 development
eslint-plugin-flowtype 8.0.3 development
eslint-plugin-i18next 5.1.2 development
eslint-plugin-import 2.26.0 development
eslint-plugin-jest 26.1.5 development
eslint-plugin-jest-dom 4.0.1 development
eslint-plugin-json 3.1.0 development
eslint-plugin-jsx-a11y 6.5.1 development
eslint-plugin-lodash 7.4.0 development
eslint-plugin-no-loops 0.3.0 development
eslint-plugin-no-secrets 0.8.9 development
eslint-plugin-node 11.1.0 development
eslint-plugin-only-ascii 0.0.0 development
eslint-plugin-only-warn 1.0.3 development
eslint-plugin-prettier 4.0.0 development
eslint-plugin-promise 6.0.0 development
eslint-plugin-react 7.29.4 development
eslint-plugin-react-hooks 4.5.0 development
eslint-plugin-react-perf 3.3.1 development
eslint-plugin-react-redux 4.0.0 development
eslint-plugin-redux-saga 1.3.2 development
eslint-plugin-security 1.5.0 development
eslint-plugin-sonarjs 0.13.0 development
eslint-plugin-unicorn 42.0.0 development
eslint-plugin-unused-imports 2.0.0 development
express 4.18.0 development
express-static-gzip 2.1.5 development
extra-watch-webpack-plugin 1.0.3 development
file-loader 6.2.0 development
fork-ts-checker-webpack-plugin 6.5.1 development
fs-extra 10.1.0 development
i18next-parser 6.3.0 development
identity-obj-proxy 3.0.0 development
is-interactive 1.0.0 development
jest 28.0.1 development
jest-axe 6.0.0 development
jest-chain 1.1.5 development
jest-extended 2.0.0 development
jest-raw-loader 1.0.1 development
jest-runner-eslint 1.0.0 development
jest-styled-components 7.0.8 development
jest-transformer-mdx 3.3.0 development
jest-watch-typeahead 1.1.0 development
js-yaml 4.1.0 development
json-autotranslate 1.10.3 development
json-loader 0.5.7 development
lodash-webpack-plugin 0.11.6 development
map.prototype.tojson 0.1.3 development
next-transpile-modules 9.0.0 development
nodemon 2.0.15 development
npm-run-all 4.1.5 development
papaparse 5.3.2 development
pkg 5.6.0 development
postcss-flexbugs-fixes 5.0.2 development
postcss-loader 6.2.1 development
postcss-preset-env 7.4.4 development
prettier 2.6.2 development
raw-loader 4.0.2 development
react-dropzone 12.1.0 development
react-query 3.38.0 development
remark-autolink-headings 6.0.1 development
remark-breaks 2.0.1 development
remark-images 2.0.0 development
remark-math 3.0.1 development
remark-slug 6.0.0 development
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rimraf 3.0.2 development
sass 1.51.0 development
set.prototype.tojson 0.1.1 development
source-map-loader 3.0.1 development
style-loader 3.3.1 development
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stylelint-config-recommended-scss 6.0.0 development
stylelint-config-standard 25.0.0 development
stylelint-config-styled-components 0.1.1 development
stylelint-declaration-block-no-ignored-properties 2.5.0 development
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stylelint-high-performance-animation 1.6.0 development
stylelint-no-indistinguishable-colors 1.3.0 development
stylelint-order 5.0.0 development
stylelint-prettier 2.0.0 development
stylelint-processor-styled-components 1.10.0 development
stylelint-scss 4.2.0 development
svgo 1.3.2 development
ts-essentials 9.1.2 development
ts-jest 27.1.4 development
ts-toolbelt 9.6.0 development
typed-redux-saga 1.4.0 development
typescript 4.6.3 development
url-loader 4.1.1 development
utility-types 3.10.0 development
webpack 5.72.0 development
webpack-cli 4.9.2 development
webpackbar 5.0.2 development
yaml-loader 0.8.0 development
animate.css 4.1.1
auspice 2.41.0
autoprefixer 10.4.5
awesomplete 1.1.5
axios 0.27.1
bootstrap 4.6.1
bowser 2.11.0
classnames 2.3.1
compare-versions 4.1.3
core-js 3.22.2
countries-list 2.6.1
css.escape 1.5.1
debug 4.3.4
fast-copy 2.1.3
fast-memoize 2.5.2
fasy 9.0.0
file-saver 2.0.5
flag-icon-css 3.5.0
formik 2.2.9
history 5.3.0
i18next 19.3.2
immutable 4.0.0
intercept-stdout 0.1.2
jschardet 3.0.0
jsonexport 3.2.0
jszip 3.9.1
lodash 4.17.21
luxon 2.3.2
marked 4.0.14
memoize-one 6.0.0
next 12.1.6
next-compose-plugins 2.2.1
numbro 2.3.6
p-memoize 4.0.4
polished 4.2.2
pretty-bytes 5.6.0
prop-types 15.8.1
re-reselect 4.0.0
react 18.1.0
react-awesome-popover 6.1.1
react-copy-to-clipboard 5.1.0
react-dom 18.1.0
react-error-boundary 3.1.4
react-file-icon 1.1.0
react-helmet 6.1.0
react-i18next 11.3.3
react-icons 4.3.1
react-if 4.1.4
react-loader-spinner 5.1.4
react-no-ssr 1.1.0
react-redux 7.2.8
react-resize-detector 7.0.0
react-select 5.3.0
react-toggle 4.1.2
react-virtualized-auto-sizer 1.0.6
react-virtualized-select 3.1.3
react-window 1.8.7
reactstrap 8.10.1
recharts 2.1.9
recoil 0.7.6
recoil-persist 4.2.0
redux 4.2.0
redux-saga 1.1.3
redux-thunk 2.4.1
reflect-metadata 0.1.13
regenerator-runtime 0.13.9
reselect 4.1.5
semver 7.3.7
serialize-javascript 6.0.0
styled-components 5.3.5
threads 1.7.0
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use-debounce 7.0.1
uuid 8.3.2
yargs 17.4.1

.github/workflows/bioconda.yml actions

actions/checkout v3 composite

packages_rs/3rdparty/typescript-definitions/Cargo.toml cargo

arrayvec 0.4.10 development
chrono 0.4 development
insta 0.6 development
proc-macro2 0.4.27 development
quote 0.6.11 development
regex 1.1.0 development
serde 1.0.87 development
serde_json 1.0.38 development
wasm-bindgen 0.2.36 development
serde 1.0.87
typescript-definitions-derive 0.1.10

packages_rs/3rdparty/typescript-definitions/typescript-definitions-derive/Cargo.toml cargo

insta 0.6.2 development
serde 1.0.87 development
cfg-if 0.1.6
failure 0.1.5
lazy_static 1.2.0
pest 2.1.0
pest_derive 2.1.0
proc-macro2 0.4.27
quote 0.6.11
regex 1.1.0
serde_derive_internals 0.24.1
syn 0.15.26

packages_rs/nextclade/Cargo.toml cargo

assert2 0.3.6 development
criterion 0.3.5 development
rstest 0.12.0 development
rstest_reuse 0.3.0 development
assert2 0.3.6
auto_ops 0.3.0
bio 0.41.0
bio-types 0.12.1
chrono 0.4.19
clap 3.1.8
clap-verbosity-flag 1.0.0
clap_complete 3.1.1
clap_complete_fig 3.1.4
color-eyre 0.6.1
csv 1.1.6
ctor 0.1.22
edit-distance 2.1.0
env_logger 0.9.0
eyre 0.6.8
flate2 1.0.24
getrandom 0.2.6
indexmap 1.8.1
itertools 0.10.3
lazy_static 1.4.0
log 0.4.16
maplit 1.0.2
num 0.4.0
num-traits 0.2.14
num_cpus 1.13.1
optfield 0.2.0
owo-colors 3.3.0
pretty_assertions 1.2.1
rayon 1.5.2
regex 1.5.5
serde 1.0.136
serde_json 1.0.79
serde_stacker 0.1.6
strum 0.24.0
strum_macros 0.24.0
tinytemplate 1.2.1
traversal 0.1.2
validator 0.14.0
zip 0.6.2

packages_rs/nextclade-cli/Cargo.toml cargo

assert2 0.3.6 development
criterion 0.3.5 development
rstest 0.12.0 development
rstest_reuse 0.3.0 development
assert2 0.3.6
clap 3.1.8
clap_complete 3.1.1
clap_complete_fig 3.1.4
color-eyre 0.6.1
comfy-table 6.0.0-rc.1
crossbeam 0.8.1
crossbeam-channel 0.5.4
ctor 0.1.22
dotenv 0.15.0
dotenv_codegen 0.15.0
eyre 0.6.8
indexmap 1.8.1
itertools 0.10.3
lazy_static 1.4.0
log 0.4.16
num_cpus 1.13.1
owo-colors 3.3.0
pretty_assertions 1.2.1
rayon 1.5.2
regex 1.5.5
reqwest 0.11.10
semver 1.0.9
serde 1.0.136
strum 0.24.0
strum_macros 0.24
url 2.2.2
zip 0.6.2

packages_rs/nextclade-web/Cargo.toml cargo

assert2 0.3.6 development
wasm-bindgen-test 0.3.29 development
assert2 0.3.6
console_error_panic_hook 0.1.7
eyre 0.6.8
getrandom 0.2.6
itertools 0.10.3
js-sys 0.3.57
log 0.4.16
serde 1.0.136
wasm-bindgen 0.2.79
wasm-logger 0.2.0
web-sys 0.3.56

docs/Dockerfile docker

continuumio/miniconda3 4.9.2 build

paper/Dockerfile docker

openjournals/paperdraft latest build

tools/osxcross/Dockerfile docker

ubuntu@sha256 31cd7bbfd36421dfd338bceb36d803b3663c1bfa87dfe6af7ba764b5bf34de05 build

Cargo.lock cargo

328 dependencies

packages_rs/nextclade-web/yarn.lock npm

2168 dependencies