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@@ -316,563 +316,3 @@ mod tests {
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Ok(())
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}
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}
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-
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-#[derive(Debug, Clone)]
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-pub struct DoradoParams {
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- pub ref_fa: String,
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- pub ref_mmi: String,
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- pub name: String,
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- pub time: String,
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- pub pod_dir: String,
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- pub samtools_view_threads: u16,
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- pub samtools_sort_threads: u16,
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-}
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-
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-// pub struct Dorado {
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-// config: Config,
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-// case: FlowCellCase,
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-// case_dir: String,
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-// time_dir: String,
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-// bam: String,
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-// start_time: SystemTime,
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-// end_time: SystemTime,
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-// is_done: bool,
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-// }
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-//
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-// impl Dorado {
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-// pub fn init(case: FlowCellCase, config: Config) -> anyhow::Result<Self> {
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-// let data_dir = &config.result_dir;
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-// let case_dir = format!("{}/{}", data_dir, case.id);
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-// let time_dir = format!("{}/{}", case_dir, case.time_point);
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-// let bam = format!("{}/{}_{}_hs1.bam", time_dir, case.id, case.time_point);
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-// debug!("Dorado init with config: {config:#?}");
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-// info!("Final BAM file: {bam}");
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-//
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-// Ok(Self {
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-// config,
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-// start_time: SystemTime::now(),
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-// end_time: SystemTime::now(),
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-// is_done: false,
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-// case_dir,
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-// time_dir,
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-// bam,
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-// case,
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-// })
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-// }
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-//
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-// // ------------------------------------------------------------------
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-// // Small helper to actually execute a shell command
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-// // ------------------------------------------------------------------
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-// fn run_shell(cmdline: &str) -> anyhow::Result<()> {
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-// info!("Running: {cmdline}");
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-// cmd!("bash", "-c", cmdline)
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-// .run()
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-// .map_err(|e| anyhow::anyhow!("Failed to run: {cmdline}\n\t{}", e.to_string()))?;
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-// Ok(())
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-// }
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-//
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-// // ------------------------------------------------------------------
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-// // Command builders (return strings)
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-// // ------------------------------------------------------------------
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-//
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-// /// minimap2 index creation (returns None if index already exists)
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-// fn create_reference_mmi_cmd(&self) -> Option<String> {
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-// if std::path::Path::new(&self.config.align.ref_mmi).exists() {
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-// None
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-// } else {
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-// Some(format!(
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-// "minimap2 -x map-ont -d {} {}",
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-// self.config.align.ref_mmi, self.config.align.ref_fa
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-// ))
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-// }
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-// }
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-//
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-// /// Dorado + samtools pipeline for basecalling + alignment
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-// fn basecall_align_cmd(&self, dorado_bin: &str) -> anyhow::Result<String> {
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-// let pod_dir = &self.case.pod_dir;
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-// let ref_fa = &self.config.align.ref_fa;
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-// let bam = &self.bam;
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-// let samtools = &self.config.align.samtools_bin;
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-// let samtools_view_threads = self.config.align.samtools_view_threads;
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-// let samtools_sort_threads = self.config.align.samtools_sort_threads;
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-// let dorado_arg = self.config.align.dorado_basecall_arg.clone();
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-//
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-// let pod_path = fs::read_dir(pod_dir)
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-// .map_err(|e| anyhow::anyhow!("Failed to read pod5 dir: {}.\n\t{e}", pod_dir.display()))?
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-// .filter_map(|p| p.ok())
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-// .map(|p| p.path())
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-// .filter(|p| p.extension().unwrap() == "pod5")
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-// .take(1)
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-// .collect::<Vec<PathBuf>>()
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-// .pop()
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-// .unwrap();
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-//
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-// let sequencing_kit = Pod5Info::from_pod5(pod_path.to_str().unwrap())
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-// .sequencing_kit
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-// .to_uppercase();
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-//
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-// let dorado = format!(
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-// "{dorado_bin} basecaller --kit-name {sequencing_kit} {dorado_arg} {} --trim all --emit-moves --reference {ref_fa}",
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-// pod_dir.display()
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-// );
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-// info!("Dorado command: {dorado}");
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-//
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-// let samtools_view = format!("{samtools} view -h -@ {samtools_view_threads} -b /dev/stdin");
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-// let samtools_sort =
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-// format!("{samtools} sort -@ {samtools_sort_threads} /dev/stdin -o {bam}");
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-//
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-// Ok(format!("{dorado} | {samtools_view} | {samtools_sort}"))
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-// }
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-//
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-// /// samtools index command
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-// fn index_cmd(&self) -> String {
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-// let t = self.config.align.samtools_view_threads.to_string();
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-// format!(
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-// "{} index -@ {t} {}",
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-// self.config.align.samtools_bin, self.bam
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-// )
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-// }
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-//
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-// /// cramino QC command
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-// fn cramino_cmd(&self) -> String {
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-// format!("cramino -t 150 --karyotype {}", self.bam)
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-// }
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-//
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-// /// modkit summary command
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-// fn modkit_cmd(&self) -> String {
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-// format!("modkit summary -t 50 {}", self.bam)
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-// }
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-//
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-// /// fastq export pipeline from BAM
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-// fn create_fastq_cmd(&self) -> String {
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-// let bam = &self.bam;
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-// let fastq = format!(
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-// "{}/{}/{}/{}_{}.fastq.gz",
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-// self.case_dir, self.case.id, self.case.time_point, self.case.id, self.case.time_point
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-// );
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-// let samtools = format!("samtools fastq -@ 150 {bam}");
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-// let crabz = format!("crabz -f bgzf - -o {fastq}");
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-// format!("{samtools} | {crabz}")
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-// }
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-//
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-// /// samtools merge command used in `merge_bam`
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-// fn merge_bam_cmd(&self, bam: &Path, into: &Path) -> String {
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-// format!(
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-// "{} merge -@ 160 -h {} {} {} {}",
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-// self.config.align.samtools_bin,
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-// bam.display(),
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-// into.display(),
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-// bam.display(),
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-// into.display() // placeholder, real tmp path is managed outside
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-// )
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-// }
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-//
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-// // mux basecall + samtools view into muxed.bam
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-// fn from_mux_basecall_cmd(
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-// config: &Config,
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-// sequencing_kit: &str,
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-// pod_dir: &str,
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-// muxed_bam: &str,
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-// ) -> String {
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-// let dorado_bin = &config.align.dorado_bin;
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-// let dorado_arg = &config.align.dorado_basecall_arg;
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-// let ref_mmi = &config.align.ref_mmi;
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-// let samtools_bin = &config.align.samtools_bin;
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-// let samtools_view_threads = config.align.samtools_view_threads;
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-//
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-// let dorado = format!(
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-// "{dorado_bin} basecaller --kit-name {sequencing_kit} {dorado_arg} {pod_dir} --emit-moves --trim all --reference {ref_mmi}"
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-// );
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-// let samtools_view =
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-// format!("{samtools_bin} view -h -@ {samtools_view_threads} -b -o {muxed_bam}");
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-// format!("{dorado} | {samtools_view}")
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-// }
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-//
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-// /// samtools split command for demux
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-// fn demux_cmd(config: &Config, muxed_bam: &str, tmp_demux_dir: &str) -> String {
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-// format!(
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-// "{} split -@ {} -f '{}/%*_%!.bam' {}",
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-// config.align.samtools_bin, config.align.samtools_view_threads, tmp_demux_dir, muxed_bam
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-// )
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-// }
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-//
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-// /// dorado aligner + samtools for realignment in from_mux
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-// fn realign_cmd(
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-// config: &Config,
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-// sequencing_kit: &str,
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-// barcode: &str,
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-// bam: &str,
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-// aligned_bam: &str,
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-// ) -> String {
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-// let dorado = format!(
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-// "{} aligner --threads {} {} {}",
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-// config.align.dorado_bin, config.align.dorado_aligner_threads, config.align.ref_fa, bam,
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-// );
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-// let samtools_view = format!(
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-// "{} view -h -@ {} -b /dev/stdin",
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-// config.align.samtools_bin, config.align.samtools_view_threads
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-// );
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-// let samtools_sort = format!(
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-// "{} sort -@ {} /dev/stdin -o {}",
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-// config.align.samtools_bin, config.align.samtools_sort_threads, aligned_bam
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-// );
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-// let _ = sequencing_kit; // not used here but kept for symmetry
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-// format!("{dorado} | {samtools_view} | {samtools_sort}")
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-// }
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-//
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-// // ------------------------------------------------------------------
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-// // Workflow methods that now *run* the commands
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-// // ------------------------------------------------------------------
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-//
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-// fn create_reference_mmi(&self) -> anyhow::Result<()> {
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-// if let Some(cmdline) = self.create_reference_mmi_cmd() {
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-// Self::run_shell(&cmdline)?;
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-// }
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-// Ok(())
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-// }
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-//
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-// fn create_directories(&self) -> anyhow::Result<()> {
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-// if !std::path::Path::new(&self.case_dir).exists() {
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-// info!("Creating directory {}", self.case_dir);
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-// fs::create_dir(&self.case_dir)?;
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-// }
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-// if !std::path::Path::new(&self.time_dir).exists() {
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-// info!("Creating directory {}", self.time_dir);
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-// fs::create_dir(&self.time_dir)?;
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-// }
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-// Ok(())
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-// }
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-//
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-// fn basecall_align(&mut self, dorado_bin: &str) -> anyhow::Result<()> {
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-// let pipe = self.basecall_align_cmd(dorado_bin)?;
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-// Self::run_shell(&pipe)
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-// .map_err(|e| anyhow::anyhow!("Failed to run pipe: {pipe}.\n\t{}", e.to_string()))
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-// }
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-//
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-// pub fn index(&self) -> anyhow::Result<()> {
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-// let cmdline = self.index_cmd();
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-// info!("Running samtools index for {}", self.bam);
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-// Self::run_shell(&cmdline)
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-// }
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-//
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-// pub fn run_cramino(&self) -> anyhow::Result<()> {
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-// let cramino_out = format!(
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-// "{}/{}_{}_hs1_cramino.txt",
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-// self.time_dir, self.case.id, self.case.time_point
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-// );
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-// info!("Quality control with cramino for BAM: {}", self.bam);
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-// let cmdline = self.cramino_cmd();
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-//
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-// let output = cmd!("bash", "-c", &cmdline)
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-// .stdout_capture()
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-// .unchecked()
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-// .run()?;
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-//
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-// fs::write(cramino_out, output.stdout)?;
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-// Ok(())
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-// }
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-//
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-// pub fn run_modkit(&self) -> anyhow::Result<()> {
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-// let mod_summary = format!(
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-// "{}/{}_{}_5mC_5hmC_summary.txt",
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-// self.time_dir, self.case.id, self.case.time_point
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-// );
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-// info!("Generating base modification summary for BAM: {}", self.bam);
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-// let cmdline = self.modkit_cmd();
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-//
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-// let output = cmd!("bash", "-c", &cmdline)
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-// .stdout_capture()
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-// .unchecked()
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-// .run()?;
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-//
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-// fs::write(mod_summary, output.stdout)?;
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-// Ok(())
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-// }
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-//
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-// pub fn create_fastq(&self) -> anyhow::Result<()> {
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-// let fastq = format!(
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-// "{}/{}/{}/{}_{}.fastq.gz",
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-// self.case_dir, self.case.id, self.case.time_point, self.case.id, self.case.time_point
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-// );
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-// if !std::path::Path::new(&fastq).exists() {
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-// let pipe = self.create_fastq_cmd();
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-// Self::run_shell(&pipe)?;
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-// }
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-// Ok(())
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-// }
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-//
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-// pub fn merge_bam(&self, bam: &Path) -> anyhow::Result<()> {
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-// let composition_a: Vec<String> = bam_composition(bam.to_string_lossy().as_ref(), 20000)?
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-// .iter()
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-// .map(|(i, _, _)| i.clone())
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-// .collect();
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-// let composition_b: Vec<String> = bam_composition(&self.bam, 20000)?
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-// .iter()
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-// .map(|(i, _, _)| i.clone())
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-// .collect();
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-// let n_id = composition_a
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-// .iter()
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-// .filter(|id| composition_b.contains(id))
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-// .count();
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-// if n_id > 0 {
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-// warn!(
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-// "{} is already merged, reads with the same run_id in the destination BAM.",
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-// self.case.id
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-// );
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-// return Ok(());
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-// }
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-//
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-// let into = PathBuf::from(&self.bam);
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-// let dir = into.parent().unwrap();
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-//
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-// let original_file = into.file_name().unwrap().to_string_lossy().to_string();
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-// let original_i = dir.join(format!("{original_file}.bai"));
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-// if !original_i.exists() {
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-// self.index()?;
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-// }
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-//
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-// let tmp_original_file = format!("{}.bam", Uuid::new_v4());
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-// let tmp_original = dir.join(tmp_original_file.clone());
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-// let tmp_original_i = dir.join(format!("{tmp_original_file}.bai"));
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-//
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-// info!("Moving {} to {}", &into.display(), &tmp_original.display());
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-// fs::rename(&into, &tmp_original)?;
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-// info!(
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-// "Moving {} to {}",
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-// &original_i.display(),
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-// &tmp_original_i.display()
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-// );
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-// fs::rename(original_i, tmp_original_i.clone())?;
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-//
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-// // real merge command with the correct tmp path
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-// let merge_cmdline = format!(
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-// "{} merge -@ 160 -h {} {} {} {}",
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-// self.config.align.samtools_bin,
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-// bam.display(),
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-// into.display(),
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-// bam.display(),
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-// tmp_original.display()
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-// );
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-// info!("Running {merge_cmdline}");
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-// Self::run_shell(&merge_cmdline)?;
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-//
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-// fs::remove_file(tmp_original)?;
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-// fs::remove_file(tmp_original_i)?;
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-// fs::remove_file(bam)?;
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-//
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-// self.index()?;
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-// Ok(())
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-// }
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-//
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-// pub fn from_mux(cases: Vec<FlowCellCase>, config: Config) -> anyhow::Result<()> {
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-// // tmp dir
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-// let tmp_dir = format!("{}/.{}", config.result_dir, Uuid::new_v4());
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-// info!("Creating tmp dir {tmp_dir}");
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-// fs::create_dir(&tmp_dir)?;
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-//
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-// // basecalling into muxed.bam
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-// let muxed_bam = format!("{tmp_dir}/muxed.bam");
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-// let pod_dir = cases[0].pod_dir.display().to_string();
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-//
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-// let muxed_pod_dir = &cases.first().unwrap().pod_dir;
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-// let pod_path = fs::read_dir(muxed_pod_dir)
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-// .map_err(|e| {
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-// anyhow::anyhow!(
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-// "Failed to read pod5 dir: {}.\n\t{e}",
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-// muxed_pod_dir.display()
|
|
|
-// )
|
|
|
-// })?
|
|
|
-// .filter_map(|p| p.ok())
|
|
|
-// .map(|p| p.path())
|
|
|
-// .filter(|p| p.extension().unwrap() == "pod5")
|
|
|
-// .take(1)
|
|
|
-// .collect::<Vec<PathBuf>>()
|
|
|
-// .pop()
|
|
|
-// .unwrap();
|
|
|
-// let sequencing_kit = Pod5Info::from_pod5(pod_path.to_str().unwrap())
|
|
|
-// .sequencing_kit
|
|
|
-// .to_uppercase();
|
|
|
-//
|
|
|
-// let basecall_pipe =
|
|
|
-// Self::from_mux_basecall_cmd(&config, &sequencing_kit, &pod_dir, &muxed_bam);
|
|
|
-// info!("Running: {basecall_pipe}");
|
|
|
-// Self::run_shell(&basecall_pipe)?;
|
|
|
-// info!("Basecalling ✅");
|
|
|
-//
|
|
|
-// // demux
|
|
|
-// let tmp_demux_dir = format!("{tmp_dir}/demuxed");
|
|
|
-// fs::create_dir(&tmp_demux_dir)?;
|
|
|
-// let demux_cmdline = Self::demux_cmd(&config, &muxed_bam, &tmp_demux_dir);
|
|
|
-// info!("Demux from {sequencing_kit} into {tmp_demux_dir}");
|
|
|
-// info!("Running: {demux_cmdline}");
|
|
|
-// Self::run_shell(&demux_cmdline)?;
|
|
|
-// info!("Demux ✅");
|
|
|
-//
|
|
|
-// for case in cases.iter() {
|
|
|
-// let barcode = case.barcode.replace("NB", "");
|
|
|
-// let bam = find_unique_file(
|
|
|
-// &tmp_demux_dir,
|
|
|
-// &format!("{sequencing_kit}_barcode{}.bam", barcode),
|
|
|
-// )?;
|
|
|
-//
|
|
|
-// let aligned_bam = if !config.align.dorado_should_realign {
|
|
|
-// bam.clone()
|
|
|
-// } else {
|
|
|
-// let aligned_bam = format!(
|
|
|
-// "{tmp_demux_dir}/{sequencing_kit}_barcode{}_aligned.bam",
|
|
|
-// barcode
|
|
|
-// );
|
|
|
-// let pipe =
|
|
|
-// Self::realign_cmd(&config, &sequencing_kit, &barcode, &bam, &aligned_bam);
|
|
|
-// info!("Running {pipe}");
|
|
|
-// Self::run_shell(&pipe)?;
|
|
|
-// info!("Alignement ✅");
|
|
|
-// aligned_bam.into()
|
|
|
-// };
|
|
|
-//
|
|
|
-// let d = Dorado::init(case.clone(), config.clone())?;
|
|
|
-// d.create_directories()?;
|
|
|
-//
|
|
|
-// if PathBuf::from(&d.bam).exists() {
|
|
|
-// info!("Merging");
|
|
|
-// d.merge_bam(&PathBuf::from(aligned_bam))?;
|
|
|
-// } else {
|
|
|
-// info!("Moving from {} to {}", bam, d.bam);
|
|
|
-// fs::rename(aligned_bam, d.bam.clone())?;
|
|
|
-// d.index()?;
|
|
|
-// }
|
|
|
-//
|
|
|
-// d.run_cramino()?;
|
|
|
-// d.run_modkit()?;
|
|
|
-// }
|
|
|
-// fs::remove_dir_all(tmp_dir)?;
|
|
|
-//
|
|
|
-// Ok(())
|
|
|
-// }
|
|
|
-//
|
|
|
-// pub fn run_pipe(&mut self) -> anyhow::Result<()> {
|
|
|
-// let start_time = std::time::SystemTime::now();
|
|
|
-// self.start_time = start_time;
|
|
|
-//
|
|
|
-// debug!("Running Dorado with config: {:#?}", self.config);
|
|
|
-// let dorado_bin = self.config.align.dorado_bin.clone();
|
|
|
-//
|
|
|
-// self.create_reference_mmi()?;
|
|
|
-// self.create_directories()?;
|
|
|
-//
|
|
|
-// info!(
|
|
|
-// "Reading {} pod5 from: {}",
|
|
|
-// self.case.time_point, self.config.pod_dir
|
|
|
-// );
|
|
|
-// let bam_path = std::path::Path::new(&self.bam);
|
|
|
-//
|
|
|
-// if !bam_path.exists() {
|
|
|
-// info!("Creating new bam file");
|
|
|
-// self.basecall_align(&dorado_bin)?;
|
|
|
-// self.index()?;
|
|
|
-// } else {
|
|
|
-// let new_bam_path = bam_path
|
|
|
-// .parent()
|
|
|
-// .unwrap()
|
|
|
-// .join(format!("{}.bam", Uuid::new_v4()));
|
|
|
-// warn!("Creating new bam {}", new_bam_path.display());
|
|
|
-//
|
|
|
-// let bam = self.bam.clone();
|
|
|
-// self.bam = new_bam_path.clone().to_string_lossy().to_string();
|
|
|
-// self.basecall_align(&dorado_bin)?;
|
|
|
-// self.bam.clone_from(&bam);
|
|
|
-// self.merge_bam(&new_bam_path)?;
|
|
|
-// }
|
|
|
-//
|
|
|
-// self.run_cramino()?;
|
|
|
-// self.run_modkit()?;
|
|
|
-// // self.create_fastq()?;
|
|
|
-//
|
|
|
-// 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();
|
|
|
-// info!(
|
|
|
-// "Dorado and Minimap2 execution time: {} seconds",
|
|
|
-// execution_time
|
|
|
-// );
|
|
|
-// self.is_done = true;
|
|
|
-//
|
|
|
-// Ok(())
|
|
|
-// }
|
|
|
-//
|
|
|
-// // from_flowcell stays mostly as-is; it just calls run_pipe/from_mux
|
|
|
-// pub fn from_flowcell(flowcell: &FlowCell, config: &Config) -> anyhow::Result<()> {
|
|
|
-// let tp_conv = |time_point: &str| -> String {
|
|
|
-// match time_point {
|
|
|
-// "normal" => config.normal_name.clone(),
|
|
|
-// "tumoral" => config.tumoral_name.clone(),
|
|
|
-// _ => panic!("Error time point name"),
|
|
|
-// }
|
|
|
-// };
|
|
|
-// use crate::collection::flowcells::FlowCellLocation::*;
|
|
|
-// let base_pod_dir = match &flowcell.location {
|
|
|
-// Local(_) => None,
|
|
|
-// Archived(pod_tar) => {
|
|
|
-// let file = File::open(pod_tar)
|
|
|
-// .map_err(|e| anyhow::anyhow!("Failed to open tar file: {pod_tar}\n\t{e}"))?;
|
|
|
-// let mut archive = tar::Archive::new(file);
|
|
|
-// info!("Un-tar of archived {pod_tar}");
|
|
|
-// archive
|
|
|
-// .unpack(&config.unarchive_tmp_dir)
|
|
|
-// .map_err(|e| anyhow::anyhow!("Failed to un-tar: {pod_tar}\n\t{e}"))?;
|
|
|
-// info!("Un-tar of archived {pod_tar} Done.");
|
|
|
-//
|
|
|
-// Some(config.unarchive_tmp_dir.to_string())
|
|
|
-// }
|
|
|
-// };
|
|
|
-//
|
|
|
-// use crate::collection::flowcells::FlowCellExperiment::*;
|
|
|
-// match &flowcell.experiment {
|
|
|
-// WGSPod5Mux(pod_dir) => {
|
|
|
-// let pod_dir = if let Some(base_pod_dir) = &base_pod_dir {
|
|
|
-// format!("{base_pod_dir}/{pod_dir}")
|
|
|
-// } else {
|
|
|
-// pod_dir.clone()
|
|
|
-// };
|
|
|
-//
|
|
|
-// let cases = flowcell
|
|
|
-// .cases
|
|
|
-// .iter()
|
|
|
-// .map(|c| FlowCellCase {
|
|
|
-// id: c.case_id.clone(),
|
|
|
-// time_point: tp_conv(&c.sample_type),
|
|
|
-// barcode: c.barcode.clone(),
|
|
|
-// pod_dir: pod_dir.clone().into(),
|
|
|
-// })
|
|
|
-// .collect();
|
|
|
-// info!("Starting basecaller for muxed pod5: {cases:#?}");
|
|
|
-//
|
|
|
-// Dorado::from_mux(cases, config.clone())?;
|
|
|
-// }
|
|
|
-// WGSPod5Demux(pod_dir) => {
|
|
|
-// let pod_dir = if let Some(base_pod_dir) = &base_pod_dir {
|
|
|
-// format!("{base_pod_dir}/{pod_dir}")
|
|
|
-// } else {
|
|
|
-// pod_dir.clone()
|
|
|
-// };
|
|
|
-//
|
|
|
-// for c in flowcell.cases.iter() {
|
|
|
-// let pod_dir = format!("{pod_dir}/barcode{}", c.barcode.replace("NB", ""));
|
|
|
-// info!("Starting basecaller for demuxed pod5: {pod_dir}");
|
|
|
-// let mut d = Dorado::init(
|
|
|
-// FlowCellCase {
|
|
|
-// id: c.case_id.clone(),
|
|
|
-// time_point: tp_conv(&c.sample_type),
|
|
|
-// barcode: c.barcode.clone(),
|
|
|
-// pod_dir: pod_dir.into(),
|
|
|
-// },
|
|
|
-// config.clone(),
|
|
|
-// )?;
|
|
|
-// d.run_pipe()?;
|
|
|
-// }
|
|
|
-// }
|
|
|
-// }
|
|
|
-//
|
|
|
-// Ok(())
|
|
|
-// }
|
|
|
-// }
|
