pandora_lib_promethion/src/callers/mod.rs

//! Variant caller integrations wired to the shared runner pattern (local/Slurm via `run!`).
//! - ClairS — <https://github.com/HKU-BAL/ClairS>
//! - DeepVariant — <https://github.com/google/deepvariant>
//! - DeepSomatic — <https://github.com/google/deepsomatic>
//! - Savana — <https://github.com/cortes-ciriano-lab/savana>
//! - Severus — <https://github.com/genome-nexus/severus> (structural variants)
//! - NanomonSV — <https://github.com/friend1ws/nanomonsv>

use crate::{
    callers::{clairs::ClairS, deep_somatic::DeepSomatic, deep_variant::DeepVariant, nanomonsv::NanomonSV, savana::Savana, severus::Severus},
    config::Config,
    pipes::{Initialize, InitializeSolo},
    runners::Run,
};

pub mod clairs;
pub mod deep_somatic;
pub mod deep_variant;
pub mod nanomonsv;
pub mod savana;
pub mod severus;

pub fn run_somatic_callers(id: &str, config: &Config) -> anyhow::Result<()> {
    // DeepVariant
    DeepVariant::initialize(id, &config.normal_name, config)?.run()?;
    DeepVariant::initialize(id, &config.tumoral_name, config)?.run()?;
    // ClairS
    ClairS::initialize(id, config)?.run()?;
    // Severus
    Severus::initialize(id, config)?.run()?;
    // Savana
    Savana::initialize(id, config)?.run()?;
    // Savana
    NanomonSV::initialize(id, config)?.run()?;
    // DeepSomatic
    DeepSomatic::initialize(id, config)?.run()?;
    Ok(())
}

#[cfg(test)]
mod tests {
    use super::*;
    use crate::helpers::test_init;

    #[test]
    fn callers_run_all() -> anyhow::Result<()> {
        test_init();
        let config = Config::default();
        run_somatic_callers("DUMCO", &config)
    }
}