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+version = "0.52.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0eee52d38c090b3caa76c563b86c3a4bd71ef1a819287c19d586d7334ae8ed66"
+
+[[package]]
+name = "windows_i686_msvc"
+version = "0.52.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "240948bc05c5e7c6dabba28bf89d89ffce3e303022809e73deaefe4f6ec56c66"
+
+[[package]]
+name = "windows_x86_64_gnu"
+version = "0.52.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "147a5c80aabfbf0c7d901cb5895d1de30ef2907eb21fbbab29ca94c5b08b1a78"
+
+[[package]]
+name = "windows_x86_64_gnullvm"
+version = "0.52.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "24d5b23dc417412679681396f2b49f3de8c1473deb516bd34410872eff51ed0d"
+
+[[package]]
+name = "windows_x86_64_msvc"
+version = "0.52.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "589f6da84c646204747d1270a2a5661ea66ed1cced2631d546fdfb155959f9ec"
+
+[[package]]
+name = "zerocopy"
+version = "0.7.35"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "1b9b4fd18abc82b8136838da5d50bae7bdea537c574d8dc1a34ed098d6c166f0"
+dependencies = [
+ "zerocopy-derive",
+]
+
+[[package]]
+name = "zerocopy-derive"
+version = "0.7.35"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "fa4f8080344d4671fb4e831a13ad1e68092748387dfc4f55e356242fae12ce3e"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn",
+]

Cargo.toml

@@ -0,0 +1,12 @@
+[package]
+name = "pandora_lib_promethion"
+version = "0.1.0"
+edition = "2021"
+
+[dependencies]
+log = "^0.4.20"
+env_logger = "^0.10.1"
+anyhow = "1.0.86"
+glob = "0.3.1"
+pandora_lib_pod5 = { git = "https://git.t0m4.fr/Thomas/pandora_lib_pod5.git" }
+regex = "1.10.5"

src/dorado.rs

@@ -0,0 +1,206 @@
+use std::{
+    fs,
+    io::{self, BufRead, BufReader, Write},
+    process::Command,
+    time::{Duration, SystemTime},
+};
+
+pub trait Run {
+    fn run(self);
+}
+
+#[derive(Debug)]
+pub struct DoradoConfig {
+    pub ref_fa: String,
+    pub ref_mmi: String,
+    pub name: String,
+    pub time: String,
+    pub pod_dir: String,
+}
+
+pub struct Dorado {
+    config: DoradoConfig,
+    start_time: SystemTime,
+    end_time: SystemTime,
+    is_done: bool,
+    log: Vec<String>
+}
+
+impl Dorado {
+    pub fn init(config: DoradoConfig) -> Self {
+        Self {
+            config,
+            start_time: SystemTime::now(),
+            end_time: SystemTime::now(),
+            is_done: false,
+            log: Vec::new(),
+        }
+    }
+}
+
+impl Run for Dorado {
+    fn run(mut self) {
+        // Start timer
+        let start_time = std::time::SystemTime::now();
+        self.start_time = start_time;
+
+        let name = &self.config.name;
+        let time = &self.config.time;
+        let pod_dir = &self.config.pod_dir;
+
+        let ref_fa = &self.config.ref_fa;
+        let ref_mmi = &self.config.ref_mmi;
+
+        let data_dir = "/data/longreads_basic_pipe";
+        let dorado_bin = "/data/tools/dorado-0.7.2-linux-x64/bin/dorado";
+        let case_dir = format!("{}/{}", data_dir, name);
+        let time_dir = format!("{}/{}", case_dir, time);
+        let bam = format!("{}/{}_{}_hs1.bam", time_dir, name, time);
+
+        if !std::path::Path::new(ref_mmi).exists() {
+            Command::new("minimap2")
+                .args(&["-x", "map-ont", "-d", ref_mmi, ref_fa])
+                .output()
+                .expect("Failed to execute minimap2");
+        }
+
+        if !std::path::Path::new(&case_dir).exists() {
+            fs::create_dir(&case_dir).expect("Failed to create case directory");
+        }
+
+        if !std::path::Path::new(&time_dir).exists() {
+            fs::create_dir(&time_dir).expect("Failed to create time directory");
+        }
+
+        println!("Reading {} pod5 from: {}", time, pod_dir);
+
+        if !std::path::Path::new(&bam).exists() {
+            let dorado_output = Command::new(dorado_bin)
+                .args(&[
+                    "basecaller",
+                    "sup,5mC_5hmC",
+                    pod_dir,
+                    "--trim",
+                    "all",
+                    "--reference",
+                    ref_mmi,
+                ])
+                .stdout(std::process::Stdio::piped())
+                .stderr(std::process::Stdio::piped())
+                .spawn()
+                .expect("Failed to execute Dorado");
+
+            if let Some(stderr) = dorado_output.stderr {
+                print_stderr(stderr, &mut self.log);
+            }
+
+            let samtools_view_output = Command::new("samtools")
+                .args(&["view", "-h", "-@ 20", "-b", "/dev/stdin"])
+                .stdin(dorado_output.stdout.unwrap())
+                .stdout(std::process::Stdio::piped())
+                .stderr(std::process::Stdio::piped())
+                .spawn()
+                .expect("Failed to execute samtools view");
+
+            if let Some(stderr) = samtools_view_output.stderr {
+                print_stderr(stderr, &mut self.log);
+            }
+
+            Command::new("samtools")
+                .args(&["sort", "-@ 30", "/dev/stdin", "-o", &bam])
+                .stdin(samtools_view_output.stdout.unwrap())
+                .output()
+                .expect("Failed to execute samtools sort");
+
+            // Create a buffer to store the output
+            // let stderr = dorado_output.stderr.take().expect("Failed to open stderr");
+            // let mut reader = std::io::BufReader::new(stderr);
+            // let mut output = String::new();
+            //
+            // loop {
+            //     // Read the output of the command
+            //     match reader.read_line(&mut output) {
+            //         Ok(0) => break, // End of output
+            //         Ok(_) => {
+            //             // Print or process the output here
+            //             print!("{}", output);
+            //             io::stderr().flush().unwrap();
+            //             // print!("{}[2J", 27 as char);
+            //             print!("\x1B[2J\x1B[1;1H");
+            //
+            //             output.clear();
+            //         }
+            //         Err(err) => {
+            //             eprintln!("Error reading from stdout: {}", err);
+            //             break;
+            //         }
+            //     }
+            //
+            //     // Optionally, you can add a delay to control refresh rate
+            //     std::thread::sleep(Duration::from_millis(100));
+            // }
+
+            Command::new("samtools")
+                .args(&["index", "-@ 150", &bam])
+                .output()
+                .expect("Failed to execute samtools index");
+        }
+
+        let cramino_out = format!("{}/{}_{}_hs1_cramino.txt", time_dir, name, time);
+        if !std::path::Path::new(&cramino_out).exists() {
+            println!("[pipe] Quality control of BAM: {}", bam);
+
+            Command::new("cramino")
+                .args(&["-t", "150", "--hist", "--checksum", "--karyotype", &bam])
+                .output()
+                .expect("Failed to execute cramino")
+                .stdout;
+        }
+
+        let mod_summary = format!("{}/{}_{}_5mC_5hmC_summary.txt", time_dir, name, time);
+        if !std::path::Path::new(&mod_summary).exists() {
+            Command::new("modkit")
+                .args(&["summary", "-t", "50", &bam])
+                .output()
+                .expect("Failed to execute modkit summary");
+        }
+
+        let fastq = format!("{}/{}/{}/{}_{}.fastq.gz", case_dir, name, time, name, time);
+        if !std::path::Path::new(&fastq).exists() {
+            Command::new("samtools")
+                .args(&["fastq", "-@ 150", &bam])
+                .stdout(std::process::Stdio::piped())
+                .spawn()
+                .expect("Failed to execute samtools fastq");
+
+            Command::new("crabz")
+                .args(&["-f", "bgzf", "-", "-o", &fastq])
+                .stdin(std::process::Stdio::piped())
+                .output()
+                .expect("Failed to execute crabz");
+        }
+
+        // Stop timer and calculate execution time
+        let end_time = std::time::SystemTime::now();
+        self.end_time = end_time;
+        let execution_time = end_time.duration_since(start_time).unwrap().as_secs_f64();
+        eprintln!(
+            "Dorado and Minimap2 execution time: {} seconds",
+            execution_time
+        );
+        self.is_done = true;
+    }
+}
+
+fn print_stderr(stderr: std::process::ChildStderr, save: &mut Vec<String>) {
+    let stderr_reader = BufReader::new(stderr);
+    for line in stderr_reader.lines() {
+        match line {
+            Ok(line) => {
+                eprintln!("{}", line);
+                save.push(line);
+            },
+            Err(err) => eprintln!("Error reading stderr: {}", err),
+        }
+    }
+}

src/lib.rs

@@ -0,0 +1,43 @@
+pub mod dorado;
+pub mod modkit;
+pub mod pod5;
+
+pub fn add(left: usize, right: usize) -> usize {
+    left + right
+}
+
+#[cfg(test)]
+mod tests {
+    use self::dorado::Run;
+
+    use super::*;
+
+    #[test]
+    fn it_works() {
+        let bam_path = "/data/longreads_basic_pipe/PARACHINI/diag/PARACHINI_diag_hs1.bam";
+        modkit::modkit(bam_path);
+    }
+
+    #[test]
+    fn run_dorado() {
+        let d = dorado::Dorado::init(dorado::DoradoConfig {
+            ref_fa: "/data/ref/hs1/chm13v2.0.fa".to_string(),
+            ref_mmi: "/data/ref/chm13v2.0.mmi".to_string(),
+            name: "CONSIGNY".to_string(),
+            time: "mrd".to_string(),
+            pod_dir: "/data/run_data/20240326-CL/CONSIGNY-MRD-NB07_RICCO-DIAG-NB08/20240326_1355_1E_PAU78333_bc25da25/pod5_pass/barcode07".to_string()
+        });
+        d.run();
+    }
+
+    #[test]
+    fn pod5() -> anyhow::Result<()> {
+        let _ =
+            env_logger::Builder::from_env(env_logger::Env::default().default_filter_or("info"))
+                .build();
+        let files = pod5::list_pod_files("/data/run_data")?;
+        println!("{files:#?}");
+        println!("{}", files.len());
+        Ok(())
+    }
+}

src/modkit.rs

@@ -0,0 +1,75 @@
+use std::{
+    io::{self, BufRead, BufReader, Write},
+    process::Command,
+    time::Duration,
+};
+
+pub fn modkit(bam_path: &str) {
+    // Command to execute your installed CLI application
+    let mut cmd = Command::new("modkit");
+
+    // Optionally, you can add arguments to the command
+    cmd.arg("summary").arg(bam_path);
+
+    // Spawn the command and obtain a handle to its output
+    let mut child = cmd
+        .stdout(std::process::Stdio::piped())
+        .spawn()
+        .expect("Failed to start command");
+
+    if let Some(stdout) = child.stdout.take() {
+        print_stdout(stdout);
+    }
+
+    // let stdout = child.stdout.take().expect("Failed to open stdout");
+
+    // Create a buffer to store the output
+    // let mut reader = std::io::BufReader::new(stdout);
+    // let mut output = String::new();
+    //
+    // loop {
+    //     // Read the output of the command
+    //     match reader.read_line(&mut output) {
+    //         Ok(0) => break, // End of output
+    //         Ok(_) => {
+    //             // Print or process the output here
+    //             print!("{}", output);
+    //             io::stdout().flush().unwrap();
+    //             // print!("{}[2J", 27 as char);
+    //             print!("\x1B[2J\x1B[1;1H");
+    //
+    //             output.clear();
+    //         }
+    //         Err(err) => {
+    //             eprintln!("Error reading from stdout: {}", err);
+    //             break;
+    //         }
+    //     }
+    //
+    //     // Optionally, you can add a delay to control refresh rate
+    //     std::thread::sleep(Duration::from_millis(100));
+    // }
+
+    // Wait for the command to finish
+    child.wait().expect("Command didn't finish");
+}
+
+fn print_stderr(stderr: std::process::ChildStderr) {
+    let stderr_reader = BufReader::new(stderr);
+    for line in stderr_reader.lines() {
+        match line {
+            Ok(line) => eprintln!("{}", line),
+            Err(err) => eprintln!("Error reading stderr: {}", err),
+        }
+    }
+}
+
+fn print_stdout(stdout: std::process::ChildStdout) {
+    let stdout_reader = BufReader::new(stdout);
+    for line in stdout_reader.lines() {
+        match line {
+            Ok(line) => eprintln!("{}", line),
+            Err(err) => eprintln!("Error reading stderr: {}", err),
+        }
+    }
+}

src/pod5.rs

@@ -0,0 +1,106 @@
+use anyhow::{anyhow, Context};
+use glob::glob;
+use log::warn;
+use pandora_lib_pod5::Pod5Info;
+use regex::Regex;
+use std::{path::PathBuf, str::FromStr, usize};
+
+#[derive(Debug)]
+pub struct Pod5 {
+    pub path: String,
+    pub pod5_type: Pod5Type,
+    pub run_name: String,
+    pub flowcell_name: String,
+}
+
+#[derive(Debug)]
+pub enum Pod5Type {
+    Raw,
+    Demuxed,
+}
+
+#[derive(Debug)]
+pub struct Pod5Config {
+    pub base_dir: String,
+    pub type_raw: String,
+    pub type_demuxed: String,
+    pub run_dir_n: u8,
+    pub flowcell_dir_n: u8,
+}
+
+impl Default for Pod5Config {
+    fn default() -> Self {
+        Self {
+            base_dir: "/data/run_data".to_string(),
+            type_raw: "/pod5/".to_string(),
+            type_demuxed: "/pod5_pass/".to_string(),
+            run_dir_n: 0,
+            flowcell_dir_n: 1,
+        }
+    }
+}
+
+impl Pod5 {
+    pub fn from_path(path: &PathBuf, config: Pod5Config) -> anyhow::Result<Self> {
+        let s = path
+            .to_str()
+            .context("Can't convert PathBuf to str {path:?}")?;
+        let pod5_type = if s.contains(&config.type_raw) {
+            Pod5Type::Raw
+        } else if s.contains(&config.type_demuxed) {
+            Pod5Type::Demuxed
+        } else {
+            return Err(anyhow!("Can't find the pod5 type {s}"));
+        };
+
+        let sr = s.replace(&config.base_dir, "");
+        let components: Vec<&str> = sr
+            .split("/")
+            .filter(|c| !c.is_empty())
+            .collect();
+
+        let run_name = components.get(config.run_dir_n as usize).context("Can't get run_name")?.to_string();
+        let flowcell_name = components.get(config.flowcell_dir_n as usize).context("Can't get flowcell_name")?.to_string();
+
+        // let info = Pod5Info::from_pod5(s);
+
+        Ok(Self {
+            path: s.to_string(),
+            pod5_type,
+            run_name,
+            flowcell_name
+        })
+    }
+}
+
+pub fn list_pod_files(dir: &str) -> anyhow::Result<Vec<Pod5>> {
+    let pattern = format!("{}/**/*.pod5", dir);
+    let mut pod_files = Vec::new();
+
+    for entry in glob(&pattern).expect("Failed to read glob pattern") {
+        match entry {
+            Ok(path) => match Pod5::from_path(&path, Pod5Config::default()) {
+                Ok(pod5) => pod_files.push(pod5),
+                Err(e) => warn!("{e}"),
+            },
+            Err(e) => warn!("Error: {:?}", e),
+        }
+    }
+
+    Ok(pod_files)
+}
+
+
+#[derive(Debug)]
+struct Run {
+    run_name: String,
+    flowcells: Vec<Flowcell>
+}
+
+#[derive(Debug)]
+struct Flowcell {
+    flowcell_name: String,
+    pod5_type: String,
+    info: Pod5Info
+}
+