dorardo up and emit-moves

src/callers/deep_somatic.rs

@@ -141,8 +141,8 @@ impl Run for DeepSomatic {
             let report = run_wait(&mut docker_run)
                 .map_err(|e| anyhow::anyhow!("Failed to run DeepSomatic for {}.\n{e}", self.id))?;
             report
-                .save_to_file(&format!("{}/deepvariant_", self.log_dir))
-                .map_err(|e| anyhow::anyhow!("Can't save DeepVariant logs.\n{e}"))?;
+                .save_to_file(&format!("{}/deepsomatic_", self.log_dir))
+                .map_err(|e| anyhow::anyhow!("Can't save DeepSomatic logs.\n{e}"))?;
         }
 
         // Keep PASS

src/commands/dorado.rs

@@ -293,7 +293,7 @@ impl Dorado {
             .to_uppercase();
 
         let dorado = format!(
-            "{dorado_bin} basecaller --kit-name {sequencing_kit} {dorado_arg} {pod_dir} --trim all --reference {ref_mmi}"
+            "{dorado_bin} basecaller --kit-name {sequencing_kit} {dorado_arg} {pod_dir} --emit-moves --trim all --reference {ref_mmi}"
         );
         let samtools_view =
             format!("samtools view -h -@ {samtools_view_threads} -b -o {muxed_bam}");

src/config.rs

@@ -160,7 +160,7 @@ impl Default for Config {
             savana_force: false,
 
             // Severus
-            severus_bin: "/data/tools/Severus/severus.py".to_string(),
+            severus_bin: "/data/tools/MySeverus/severus.py".to_string(),
             severus_threads: 32,
             vntrs_bed: "/data/ref/hs1/vntrs_chm13.bed".to_string(),
             severus_pon: "/data/ref/hs1/PoN_1000G_chm13.tsv.gz".to_string(),
@@ -232,7 +232,8 @@ pub struct AlignConfig {
 impl Default for AlignConfig {
     fn default() -> Self {
         Self {
-            dorado_bin: "/data/tools/dorado-0.9.1-linux-x64/bin/dorado".to_string(),
+            dorado_bin: "/data/tools/dorado-1.0.0-linux-x64/bin/dorado".to_string(),
+            // dorado_bin: "/data/tools/dorado-0.9.1-linux-x64/bin/dorado".to_string(),
             dorado_basecall_arg: "-x 'cuda:0,1,2,3' sup,5mC_5hmC".to_string(),
             // to specify cuda devices (exclude the T1000)
             ref_fa: "/data/ref/hs1/chm13v2.0.fa".to_string(),
@@ -397,6 +398,8 @@ impl Config {
     pub fn deepsomatic_passed_vcf(&self, id: &str) -> String {
         format!(
             "{}/{}_{}_DeepSomatic_PASSED.vcf.gz",
+            // ERROR replace but before rename actually misplaced 
+            // self.deepsomatic_output_dir(id),
             self.deepvariant_normal_output_dir(id),
             id,
             self.tumoral_name

src/lib.rs

@@ -286,9 +286,9 @@ mod tests {
     }
 
     #[test]
-    fn nanomddonsv_solo() -> anyhow::Result<()> {
+    fn nanomonsv_solo() -> anyhow::Result<()> {
         init();
-        NanomonSVSolo::initialize("BRETON", "diag", Config::default())?.run()
+        NanomonSVSolo::initialize("GRAND", "diag", Config::default())?.run()
     }
 
     // cargo test run -- --nocapture; ~/run_scripts/notify_finish.sh &
@@ -466,14 +466,14 @@ mod tests {
     #[test]
     fn run_severus() -> anyhow::Result<()> {
         init();
-        Severus::initialize("CAMEL", Config::default())?.run()
+        Severus::initialize("PONSOT", Config::default())?.run()
     }
 
-    #[test]
-    fn run_severus_solo() -> anyhow::Result<()> {
-        init();
-        SeverusSolo::initialize("CAMEL","diag", Config::default())?.run()
-    }
+    // #[test]
+    // fn run_severus_solo() -> anyhow::Result<()> {
+    //     init();
+    //     SeverusSolo::initialize("CAMEL","diag", Config::default())?.run()
+    // }
 
     #[test]
     fn run_savana() -> anyhow::Result<()> {
@@ -1101,7 +1101,7 @@ let variant: VcfVariant = row.parse()?;
     #[test]
     fn somatic_cases() -> anyhow::Result<()> {
         init();
-        let id = "ACHITE";
+        let id = "SABER";
         let config = Config { somatic_pipe_force: true, ..Default::default() };
         match SomaticPipe::initialize(id, config)?.run() {
             Ok(_) => (),