give a sheet now handles writing

Cargo.toml

@@ -17,6 +17,8 @@ clap-verbosity-flag = "2.2.0"
 color-eyre = "0.6.3"
 glob = "0.3.1"
 rayon = "1.9.0"
+regex = "1.10.4"
+tracing = "0.1.40"
 
 [profile.dev.package.backtrace]
 opt-level = 3

src/cli.rs

@@ -57,10 +57,10 @@ pub enum Commands {
         /// The sequencing platform where FASTQs came from
         #[arg(short, long, required = true)]
         platform: SeqPlatform,
-        // /// Output file prefix (the part before the `_samplesheet.csv`)
-        // #[arg(short, long, required = false)]
-        // output_file: Option<String>,
 
+        /// Output file prefix (the part before the `_samplesheet.csv`)
+        #[arg(short, long, required = false, default_value = None)]
+        output_prefix: Option<String>,
         // /// Check a pre-existing samplesheet
         // #[arg(short, long, required = false, default_value = "samplesheet.csv")]
         // check: Option<String>,
@@ -81,5 +81,9 @@ pub enum Commands {
         /// the number of cells expected
         #[arg(short, long, required = true)]
         expected_cells: i64,
+
+        /// Output file prefix (the part before the `_samplesheet.csv`)
+        #[arg(short, long, required = false, default_value = None)]
+        output_prefix: Option<String>,
     },
 }

src/main.rs

@@ -15,15 +15,17 @@ fn main() -> Result<()> {
             input_dir,
             fastq_ext,
             platform,
+            output_prefix,
         }) => {
-            viralrecon::give_a_sheet(input_dir, fastq_ext, platform)?;
+            viralrecon::give_a_sheet(input_dir, fastq_ext, platform, output_prefix)?;
         }
         Some(Commands::Scrnaseq {
             input_dir,
             fastq_ext,
             expected_cells,
+            output_prefix,
         }) => {
-            scrnaseq::give_a_sheet(input_dir, fastq_ext, &expected_cells)?;
+            scrnaseq::give_a_sheet(input_dir, fastq_ext, &expected_cells, output_prefix)?;
         }
         None => {
             eprintln!("{}\n", cli::INFO);

src/scrnaseq.rs

@@ -1,24 +1,36 @@
+use regex::Regex;
 use std::{collections::HashSet, ffi::OsStr, path::Path, rc::Rc};
+use tracing::warn;
 
+use crate::utils::write_lines;
 pub use crate::viralrecon::find_files;
 use color_eyre::eyre::Result;
 
 fn retrieve_samples(file_paths: &[Rc<Path>]) -> HashSet<Rc<str>> {
+    let illumina_pattern = Regex::new(r"_L\d{3}_R\d_\d{3}\.fastq\.gz$").unwrap();
+
     file_paths
         .into_iter()
         .map(|path| {
             Rc::from(
                 path.file_name()
                     .unwrap_or(OsStr::new(""))
                     .to_string_lossy()
-                    .replace("_L001_R1_001.fastq.gz", "")
-                    .replace("_L001_R2_001.fastq.gz", "")
                     .as_ref(),
             )
         })
+        .map(|x| Rc::from(illumina_pattern.replace_all(&x, "").to_string()))
         .collect()
 }
 
+fn check_sample_ids(sample_ids: &HashSet<Rc<str>>) {
+    for id in sample_ids {
+        if id.chars().count() >= 64 {
+            warn!("Sample id {} is 64 or more characters long, which is maximum enforced by some of the SCRNAseq aligners. SCRNAseq may crash if you don't manually shorten the id in your samplesheet.", id)
+        }
+    }
+}
+
 fn collect_per_sample(
     sample_id: &Rc<str>,
     fastq_paths: &[Rc<Path>],
@@ -52,7 +64,7 @@ fn collect_per_sample(
     Ok(vec![sample_id, fastq1, fastq2, &cell_str].join(","))
 }
 
-pub fn concat_lines(
+fn concat_lines(
     sample_ids: &HashSet<Rc<str>>,
     fastq_paths: &[Rc<Path>],
     expected_cells: &i64,
@@ -63,14 +75,21 @@ pub fn concat_lines(
         .collect::<Vec<String>>()
 }
 
-pub fn give_a_sheet(input_dir: &Path, fastq_ext: &str, expected_cells: &i64) -> Result<()> {
+pub fn give_a_sheet(
+    input_dir: &Path,
+    fastq_ext: &str,
+    expected_cells: &i64,
+    output_prefix: &Option<String>,
+) -> Result<()> {
+    // find the FASTQ files and separate out the unique sample IDs
     let fastq_paths = find_files(input_dir, fastq_ext)?;
     let sample_ids: HashSet<Rc<str>> = retrieve_samples(&fastq_paths);
-    let lines = concat_lines(&sample_ids, &fastq_paths, expected_cells);
 
-    for line in lines {
-        println!("{}", line)
-    }
+    // check the sample IDs for any that are too long
+    check_sample_ids(&sample_ids);
 
-    Ok(())
+    // concatenate and write the lines
+    let lines = concat_lines(&sample_ids, &fastq_paths, expected_cells);
+    let header = "sample,fastq_1,fastq_2,expected_cells";
+    write_lines(&lines, header, output_prefix)
 }

src/utils.rs

@@ -1,4 +1,5 @@
-use std::{collections::HashSet, fmt, path::Path, rc::Rc};
+use color_eyre::eyre::Result;
+use std::{collections::HashSet, fmt, fs::File, io::BufWriter, io::Write, path::Path, rc::Rc};
 
 use clap::ValueEnum;
 
@@ -26,3 +27,20 @@ impl fmt::Display for SeqPlatform {
 pub trait RetrieveSampleIds {
     fn retrieve_samples(&self, file_paths: &[Rc<Path>]) -> HashSet<Rc<str>>;
 }
+
+pub fn write_lines(lines: &[String], header: &str, output_prefix: &Option<String>) -> Result<()> {
+    let out_name = match output_prefix {
+        Some(prefix) => format!("{}_samplesheet.csv", prefix),
+        None => String::from("samplesheet.csv"),
+    };
+
+    let file = File::create(out_name)?;
+    let mut buf_writer = BufWriter::new(file);
+
+    writeln!(buf_writer, "{}", header)?;
+    lines
+        .into_iter()
+        .try_for_each(|line| writeln!(buf_writer, "{}", line))?;
+
+    Ok(())
+}

src/viralrecon.rs

@@ -1,6 +1,7 @@
-use crate::utils::SeqPlatform;
+use crate::utils::{write_lines, SeqPlatform};
 use color_eyre::eyre::Result;
 use glob::glob;
+use regex::Regex;
 use std::{collections::HashSet, ffi::OsStr, path::Path, rc::Rc};
 
 use crate::utils::RetrieveSampleIds;
@@ -23,19 +24,21 @@ impl RetrieveSampleIds for SeqPlatform {
     fn retrieve_samples(&self, file_paths: &[Rc<Path>]) -> HashSet<Rc<str>> {
         match self {
             // handle paired end FASTQ files for Illumina
-            SeqPlatform::Illumina => file_paths
-                .into_iter()
-                .map(|path| {
-                    Rc::from(
-                        path.file_name()
-                            .unwrap_or(OsStr::new(""))
-                            .to_string_lossy()
-                            .replace("_L001_R1_001.fastq.gz", "")
-                            .replace("_L001_R2_001.fastq.gz", "")
-                            .as_ref(),
-                    )
-                })
-                .collect(),
+            SeqPlatform::Illumina => {
+                let illumina_pattern = Regex::new(r"_L\d{3}_R\d_\d{3}\.fastq\.gz$").unwrap();
+                file_paths
+                    .into_iter()
+                    .map(|path| {
+                        Rc::from(
+                            path.file_name()
+                                .unwrap_or(OsStr::new(""))
+                                .to_string_lossy()
+                                .as_ref(),
+                        )
+                    })
+                    .map(|x| Rc::from(illumina_pattern.replace_all(&x, "").to_string()))
+                    .collect()
+            }
             // handle per-barcode single FASTQs for Nanopore
             SeqPlatform::Nanopore => file_paths
                 .into_iter()
@@ -121,14 +124,15 @@ pub fn concat_lines(
         .collect::<Vec<String>>()
 }
 
-pub fn give_a_sheet(input_dir: &Path, fastq_ext: &str, platform: &SeqPlatform) -> Result<()> {
+pub fn give_a_sheet(
+    input_dir: &Path,
+    fastq_ext: &str,
+    platform: &SeqPlatform,
+    output_prefix: &Option<String>,
+) -> Result<()> {
     let fastq_paths = find_files(input_dir, fastq_ext)?;
     let sample_ids: &HashSet<Rc<str>> = &platform.retrieve_samples(&fastq_paths);
     let lines = concat_lines(sample_ids, &fastq_paths, platform);
-
-    for line in lines {
-        eprintln!("{}", line);
-    }
-
-    Ok(())
+    let header = "sample,fastq_1,fastq_2";
+    write_lines(&lines, header, output_prefix)
 }