up

src/collection/mod.rs

@@ -50,7 +50,7 @@ impl Default for CollectionsConfig {
             corrected_fc_path: "/data/flow_cells.tsv".to_string(),
             result_dir: "/data/longreads_basic_pipe".to_string(),
             dict_file: "/data/ref/hs1/chm13v2.0.dict".to_string(),
-            min_diag_cov: 15.0,
+            min_diag_cov: 12.0,
             min_mrd_cov: 10.0,
         }
     }

src/lib.rs

@@ -18,6 +18,8 @@ lazy_static! {
 
 #[cfg(test)]
 mod tests {
+    use log::info;
+
     use self::{callers::deep_variant::DeepVariantConfig, collection::pod5::{FlowCellCase, Pod5Collection}, commands::dorado, config::Config};
     use super::*;
     use crate::{callers::{clairs::{ClairS, ClairSConfig}, deep_variant::DeepVariant, nanomonsv::{NanomonSV, NanomonSVConfig}}, collection::{bam::{self, BamType}, run_tasks, variants::VariantsCollection, vcf::VcfCollection, Collections, CollectionsConfig}, commands::{bcftools::{bcftools_keep_pass, BcftoolsConfig}, dorado::Dorado}};
@@ -122,12 +124,14 @@ mod tests {
         let mut collections = Collections::new(
             CollectionsConfig::default()
         )?;
+        info!("Runing todo with config: {:#?}", collections);
         collections.todo()?;
         println!("{:#?}", collections.tasks);
         println!("{}", collections.tasks.len());
         Ok(())
     }
 
+    // export RUST_LOG="debug"
     #[test_log::test]
     fn run_t() -> anyhow::Result<()> {
         run_tasks(CollectionsConfig::default())