update

src/collection/mod.rs

@@ -63,9 +63,9 @@ impl Collections {
 
     pub fn todo(&mut self, min_diag_cov: f32, min_mrd_cov: f32) {
         info!("Looking for base calling tasks...");
+
         let mut tasks = Vec::new();
         // let mut to_demux = Vec::new();
-        //
         // for run in self.pod5.runs.iter() {
         //     for fc in run.flowcells.iter() {
         //         let acq_id = fc.pod5_info.acquisition_id.clone();
@@ -208,6 +208,10 @@ impl Collections {
                 }
             }
         });
+
+
+        // 
+
         let mut hs = HashMap::new();
         tasks.into_iter().for_each(|t| {
             hs.insert(t.to_string(), t);

src/commands/dorado.rs

@@ -382,7 +382,7 @@ impl Dorado {
 
         info!("Running Dorado with params: {:#?}", self.config);
 
-        let dorado_bin = "/data/tools/dorado-0.7.2-linux-x64/bin/dorado";
+        let dorado_bin = self.config.align.dorado_bin.clone();
 
         self.create_reference_mmi()?;
         self.create_directories()?;
@@ -395,7 +395,7 @@ impl Dorado {
 
         if !bam_path.exists() {
             info!("Creating new bam file");
-            self.basecall_align(dorado_bin)?;
+            self.basecall_align(&dorado_bin)?;
         } else {
             // check if merge before call
             let new_bam_path = bam_path
@@ -406,7 +406,7 @@ impl Dorado {
 
             let bam = self.bam.clone();
             self.bam = new_bam_path.clone().to_string_lossy().to_string();
-            self.basecall_align(dorado_bin)?;
+            self.basecall_align(&dorado_bin)?;
             self.bam.clone_from(&bam);
             self.merge_bam(&new_bam_path)?;
         }

src/config.rs

@@ -28,7 +28,7 @@ pub struct AlignConfig {
 impl Default for AlignConfig {
     fn default() -> Self {
         Self {
-            dorado_bin: "/data/tools/dorado-0.7.2-linux-x64/bin/dorado".to_string(),
+            dorado_bin: "/data/tools/dorado-0.7.3-linux-x64/bin/dorado".to_string(),
             dorado_basecall_arg: "sup,5mC_5hmC".to_string(),
             ref_fa: "/data/ref/hs1/chm13v2.0.fa".to_string(),
             ref_mmi: "/data/ref/chm13v2.0.mmi".to_string(),