info

ok_cases.tsv

@@ -1,140 +0,0 @@
-
-running 1 test
-test tests::bam_ok has been running for over 60 seconds
-ACHITE	diag
-ACHITE	mrd
-ALLEMAN	mrd
-ALLEMAND	diag
-AOUF	diag
-AOUF	mrd
-AUBERT	diag
-AUBERT	mrd
-BAFFREAU	diag
-BAFFREAU	mrd
-BAILLEUL	diag
-BAILLEUL	mrd
-BECERA	mrd
-BECERRA	diag
-BECERRA	mrd
-BELARBI	diag
-BELARBI	mrd
-BENDENMOUN	diag
-BENDENMOUN	mrd
-BENGUIRAT	diag
-BENGUIRAT	mrd
-BERNIER	diag
-BERNIER	mrd
-BOUDJELTHIA	diag
-BOUDJELTHIA	mrd
-CAMARA	diag
-CAMARA	mrd
-CHENU	diag
-CHENU	mrd
-COLLE	diag
-COLLE	mrd
-CONSIGNY	diag
-CONSIGNY	mrd
-DAHAN	diag
-DAHAN	diag
-DAHAN	diag
-DAHAN	mrd
-DAHAN	mrd
-DOUYERE	diag
-ELKLIFI	diag
-ELKLIFI	mrd
-FALZONE	diag
-FALZONE	mrd
-FAVOT	diag
-FAVOT	mrd
-FERATI	diag
-FERATI	mrd
-FRANIATTE	diag
-FRANIATTE	mrd
-GABELLE	diag
-GABELLE	mrd
-GALLET	diag
-GALLET	mrd
-GARAGNON	diag
-GARAGNON	mrd
-GEORGIEV	diag
-GEORGIEV	mrd
-GRAY	diag
-GRAY	diag
-GRAY	mrd
-GRAY	mrd
-HAMROUNE	diag
-HAMROUNE	mrd
-HATTAB	diag
-HATTAB	mrd
-HENAUX	diag
-HENAUX	mrd
-HEORHIICHUK	diag
-HEORHIICHUK	mrd
-HURION	diag
-HURION	mrd
-IQBAL	diag
-IQBAL	mrd
-JOLIVET	diag
-JOLIVET	mrd
-KENNOUCHE	mrd
-KHABER	diag
-KHABER	mrd
-KHABER	mrd
-LEV	diag
-LEVASSEUR	diag
-LEVASSEUR	mrd
-MACCAGN	diag
-MACCAGN	mrd
-MACCAGN	mrd
-MANCUS	diag
-MANCUS	mrd
-MEDDAH	diag
-MEDDAH	mrd
-MERY	diag
-MERY	mrd
-MICHELAS	diag
-MICHELAS	mrd
-MIGAUD	diag
-MIGAUD	mrd
-MOREAU	diag
-MOREAU	mrd
-MORIN	diag
-MORIN	mrd
-NAJAR	diag
-NAJAR	mrd
-PARACHINI	diag
-PARACHINI	mrd
-PASSARD	diag
-PASSARD	mrd
-PENN	diag
-PENN	mrd
-RICCO	diag
-RICCO	mrd
-RIVOALEN	diag
-RIVOALEN	mrd
-ROBIN	diag
-ROBIN	mrd
-ROZIER	diag
-ROZIER	mrd
-SABER	diag
-SABER	mrd
-SALICETTO	diag
-SALICETTO	mrd
-SAUTRE	diag
-SAUTRE	mrd
-SPINATO	diag
-SPINATO	mrd
-TAOUS	diag
-TAOUS	mrd
-THETE	diag
-THETE	mrd
-VAUTRIN	diag
-VAUTRIN	mrd
-VEILLEUR	diag
-VEILLEUR	mrd
-VILI	diag
-VILI	mrd
-test tests::bam_ok ... ok
-
-test result: ok. 1 passed; 0 failed; 0 ignored; 0 measured; 13 filtered out; finished in 68.05s
-

src/collection/mod.rs

@@ -52,7 +52,7 @@ 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: 12.0,
+            min_diag_cov: 11.0,
             min_mrd_cov: 10.0,
             id_black_list: Vec::default(),
         }

src/commands/dorado.rs

@@ -201,7 +201,10 @@ impl Dorado {
             .filter(|id| composition_b.contains(id))
             .count();
         if n_id > 0 {
-            warn!("{} is already merged", self.case.id);
+            warn!(
+                "{} is already merged, reads with the same run_id in the destination BAM.",
+                self.case.id
+            );
             return Ok(());
         }
 
@@ -328,7 +331,10 @@ impl Dorado {
                 "{} trim {bam} | samtools view -h -@ {} -b /dev/stdin -o {trimmed_bam}",
                 config.align.dorado_bin, &config.align.samtools_view_threads
             );
+
+            info!("Running: {pipe}");
             cmd!("bash", "-c", pipe).run()?;
+            info!("Trim ✅");
 
             // Align
             let aligned_bam = format!(
@@ -348,15 +354,16 @@ impl Dorado {
                 &config.align.samtools_sort_threads
             );
             let pipe = format!("{dorado} | {samtools_view} | {samtools_sort}");
-            info!("Running {pipe}");
 
+            info!("Running {pipe}");
             cmd!("bash", "-c", pipe).run()?;
+            info!("Alignement ✅");
 
             let d = Dorado::init(case.clone(), config.clone())?;
             d.create_directories()?;
 
             if PathBuf::from(&d.bam).exists() {
-                info!("merge");
+                info!("Merging");
                 d.merge_bam(&PathBuf::from(aligned_bam))?;
             } else {
                 info!("Moving from {} to {}", bam, d.bam);