Open Issues Need Help
View All on GitHubAI Summary: When searching for datasets on the Clades website, the search results list automatically scrolls to the currently selected dataset at the bottom, rather than displaying the relevant search results at the top. This behavior makes it difficult for users to see and select the datasets matching their search query, hindering usability.
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
AI Summary: A user encountered an "Internal Error: Dataset not found: 'undefined'" in Nextclade version 3.18.1, indicating a programming mistake where a dataset name was expected but was `undefined`. The error occurred within the web application, with the call stack pointing to JavaScript files related to export functionality and the framework.
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
AI Summary: The user encountered an error with `yarn install` while setting up the Nextclade webserver locally. They suggest adding `npm install -g yarn` to the developer guide before step 6 to ensure Yarn is properly installed globally, which should resolve the issue.
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
AI Summary: The Nextclade Newick writer omits the trailing semicolon, which is a common convention and expected by some parsers like R's ape package, causing them to fail. The request is to always include the semicolon to improve compatibility with other Newick readers.
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
AI Summary: The Nextclade CLI displays an error message where a file path appears with two sets of quotes (e.g., `'"/tmp/path"'`). This double quoting is confusing to users, as it suggests they might be incorrectly passing the path with quotes. The issue attributes this to the debug formatting (`{:#?}`) used in the error message combined with existing string literals.
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
AI Summary: The issue is a Next.js build error related to importing a WebAssembly module (nextclade-wasm_bg.wasm) within the Nextclade web application. The error message indicates an incompatibility between the ESM (ECMAScript module) import method used and how the WebAssembly module is being handled. The task involves troubleshooting this build error, likely by adjusting the import statement or configuration to correctly integrate the WebAssembly module into the Next.js application.
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
AI Summary: Investigate why Nextclade's output `attributes` contain URL-encoded semicolons, despite the GFF3 files being the source. Determine if this is a bug in Nextclade's decoding process or an issue elsewhere in the pipeline, and provide a solution or workaround.
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
AI Summary: The task is to debug a potential bug in Nextclade's alignment algorithm. The bug causes a `hit_boundary` warning when trailing indels are present at the end of a simple stripe alignment. The solution might involve modifying the `score_matrix` function to avoid considering trailing indels as boundary hits, similar to a fix implemented in a related project.
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
AI Summary: The task is to debug a Nextclade (version 3.15.1) issue where a cached or incorrectly configured dataset URL ('http://localhost:3000') causes analysis results to not display and export to fail with an 'Internal Error: Dataset not found' message. The solution involves identifying and removing the cached URL setting, potentially clearing browser cache, and verifying the issue is resolved. The debug information includes the error message, stack trace, and user agent details.
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement