up bcftools

README.md

@@ -1,4 +1,9 @@
 
+
+## Install
+
+### Dependencies
+
 For building required HTSlib:
 ```
 sudo apt install cmake libclang-dev
@@ -6,13 +11,10 @@ sudo apt install cmake libclang-dev
 ```
 
 * minimap2 
-* samtools
-* dorado
-* modkit 
-```
-cargo install --git https://github.com/nanoporetech/modkit.git
-```
-
-for variants:
+* (samtools)[https://www.htslib.org/download/]
+* (dorado)[https://github.com/nanoporetech/dorado]
+* (bcftools)[https://www.htslib.org/download/]
+* (modkit)[https://github.com/nanoporetech/modkit]
 * VEP: cf pandora_lib_variants for VEP install
 
+###

src/callers/deep_variant.rs

@@ -24,7 +24,7 @@ impl Default for DeepVariantConfig {
             model_type: "ONT_R104".to_string(),
             result_dir: "/data/longreads_basic_pipe".to_string(),
             reference: "/data/ref/hs1/chm13v2.0.fa".to_string(),
-            bcftools: "/data/tools/bcftools-1.18/bcftools".to_string(),
+            bcftools: "/data/tools/bcftools-1.21/bcftools".to_string(),
         }
     }
 }
@@ -85,7 +85,7 @@ impl DeepVariant {
                 &format!("{}:/output", self.output_dir),
                 &format!("google/deepvariant:{}", self.config.bin_version),
                 "/opt/deepvariant/bin/run_deepvariant",
-                "--model_type=ONT_R104",
+                &format!("--model_type={}", self.config.model_type),
                 "--ref",
                 &self.config.reference,
                 "--reads",

src/callers/nanomonsv.rs

@@ -1,8 +1,4 @@
-use std::{
-    fs,
-    path::Path,
-    thread,
-};
+use std::{fs, path::Path, thread};
 
 use log::info;
 
@@ -149,7 +145,9 @@ impl NanomonSV {
 
         let vcf_passed = format!("{diag_out_prefix}_nanomonsv_PASSED.vcf.gz");
         if !Path::new(&vcf_passed).exists() {
-            let report  = bcftools_keep_pass(&diag_result_vcf, &vcf_passed, BcftoolsConfig::default()).unwrap();
+            let report =
+                bcftools_keep_pass(&diag_result_vcf, &vcf_passed, BcftoolsConfig::default())
+                    .unwrap();
             report
                 .save_to_file(&format!("{}/bcftools_pass_", self.log_dir,))
                 .unwrap();

src/collection/mod.rs

@@ -602,13 +602,13 @@ impl fmt::Display for CollectionsTasks {
         use CollectionsTasks::*;
 
         match self {
-            Align(case) => write!(f, "Alignment task for: {} {}", case.id, case.time_point),
+            Align(case) => write!(f, "Alignment task for: {} {} {}", case.id, case.time_point, case.barcode),
             DemuxAlign(cases) => write!(
                 f,
                 "Demultiplex and alignment task for: {}",
                 cases
                     .iter()
-                    .map(|c| format!("{} {}", c.id, c.time_point))
+                    .map(|c| format!("{} {} {}", c.id, c.time_point, c.barcode))
                     .collect::<Vec<String>>()
                     .join(", ")
             ),

src/commands/bcftools.rs

@@ -12,7 +12,7 @@ pub struct BcftoolsConfig {
 impl Default for BcftoolsConfig {
     fn default() -> Self {
         Self {
-            bin: "bcftools".to_string(),
+            bin: "/data/tools/bcftools-1.21/bcftools".to_string(),
             threads: 20,
         }
     }

src/commands/dorado.rs

@@ -144,7 +144,7 @@ impl Dorado {
             "{}/{}_{}_hs1_cramino.txt",
             self.time_dir, self.case.id, self.case.time_point
         );
-        info!("Quality control with cramino of BAM: {}", self.bam);
+        info!("Quality control with cramino for BAM: {}", self.bam);
         let output = duct::cmd!("cramino", "-t", "150", "--karyotype", &self.bam)
             .stdout_capture()
             .unchecked()