feat(cli): add "sort-and-run" subcommand

Cargo.toml

@@ -41,6 +41,7 @@ console_error_panic_hook = "=0.1.7"
 criterion = { version = "=0.5.1", features = ["html_reports"] }
 crossbeam = "=0.8.2"
 crossbeam-channel = "=0.5.8"
+crossbeam-skiplist = "=0.1.3"
 csv = "=1.2.2"
 ctor = "=0.2.2"
 derive_more = "=0.99.17"

packages/nextclade-cli/Cargo.toml

@@ -25,6 +25,7 @@ color-eyre = { workspace = true }
 comfy-table = { workspace = true }
 crossbeam = { workspace = true }
 crossbeam-channel = { workspace = true }
+crossbeam-skiplist = { workspace = true }
 ctor = { workspace = true }
 dotenv = { workspace = true }
 dotenv_codegen = { workspace = true }

packages/nextclade-cli/src/cli/mod.rs

@@ -4,6 +4,7 @@ pub mod nextclade_dataset_list;
 pub mod nextclade_loop;
 pub mod nextclade_ordered_writer;
 pub mod nextclade_read_annotation;
+pub mod nextclade_run_sort_and_analysis;
 pub mod nextclade_seq_sort;
 pub mod print_help_markdown;
 pub mod verbosity;

packages/nextclade-cli/src/cli/nextclade_cli.rs

@@ -2,6 +2,7 @@ use crate::cli::nextclade_dataset_get::nextclade_dataset_get;
 use crate::cli::nextclade_dataset_list::nextclade_dataset_list;
 use crate::cli::nextclade_loop::nextclade_run;
 use crate::cli::nextclade_read_annotation::nextclade_read_annotation;
+use crate::cli::nextclade_run_sort_and_analysis::nextclade_run_sort_and_analysis;
 use crate::cli::nextclade_seq_sort::nextclade_seq_sort;
 use crate::cli::print_help_markdown::print_help_markdown;
 use crate::cli::verbosity::Verbosity;
@@ -95,6 +96,8 @@ pub enum NextcladeCommands {
   /// For short help type: `nextclade -h`, for extended help type: `nextclade --help`. Each subcommand has its own help, for example: `nextclade sort --help`.
   Sort(Box<NextcladeSortArgs>),
 
+  SortAndRun(Box<NextcladeSortArgs>),
+
   /// Read genome annotation and present it in Nextclade's internal formats. This is mostly only useful for Nextclade maintainers and the most curious users. Note that these internal formats have no stability guarantees and can be changed at any time without notice.
   ///
   /// For short help type: `nextclade -h`, for extended help type: `nextclade --help`. Each subcommand has its own help, for example: `nextclade sort --help`.
@@ -442,7 +445,7 @@ pub struct NextcladeRunInputArgs {
 }
 
 #[allow(clippy::struct_excessive_bools)]
-#[derive(Parser, Debug, Clone)]
+#[derive(Parser, Debug, Clone, Default)]
 pub struct NextcladeRunOutputArgs {
   /// REMOVED. Use `--output-all` instead
   #[clap(long)]
@@ -1128,6 +1131,7 @@ pub fn nextclade_parse_cli_args() -> Result<(), Report> {
       }
     },
     NextcladeCommands::Sort(seq_sort_args) => nextclade_seq_sort(&seq_sort_args),
+    NextcladeCommands::SortAndRun(args) => nextclade_run_sort_and_analysis(&args),
     NextcladeCommands::ReadAnnotation(read_annotation_args) => nextclade_read_annotation(&read_annotation_args),
   }
 }

packages/nextclade-cli/src/cli/nextclade_loop.rs

@@ -17,6 +17,7 @@ use nextclade::tree::tree_builder::graph_attach_new_nodes_in_place;
 use nextclade::types::outputs::NextcladeOutputs;
 use nextclade::utils::option::OptionMapRefFallible;
 
+#[derive(Debug)]
 pub struct NextcladeRecord {
   pub index: usize,
   pub seq_name: String,