Update deps

Author: nikothomas

Cargo.lock

@@ -1,17 +1,17 @@
 [package]
 name = "windchime"
-version = "0.0.2"
+version = "0.0.3"
 edition = "2021"
 
 [dependencies]
 # Command-line argument parsing
 clap = { version = "4.3", features = ["derive"] }
 
 # For color-coded terminal output
-colored = "2.0"
+colored = "3.0"
 
 # For interactive wizard prompts
-dialoguer = "0.10"
+dialoguer = "0.11"
 
 # For progress bars and spinners
 indicatif = "0.17.11"
@@ -36,7 +36,3 @@ chrono = "0.4"
 csv = "1.1"
 serde = { version = "1.0.217", features = ["derive"] }
 once_cell = "1.20.2"
-
-[profile.release]
-# Optional: If you want faster performance on large data
-opt-level = 3

Cargo.toml

@@ -555,9 +555,12 @@ pub fn run_pipeline(
         let pr2_extracts_qza = out_path("db/pr2/pr2_extracts.qza");
         if !skip_existing || !Path::new(&pr2_extracts_qza).exists() {
             run_step("Extracting pr2 reads", || {
-                // For illustration, we'll pick some generic primer F/R here:
-                let primer_f = "GTGYCAGCMGCCGCGGTAA";
-                let primer_r = "CCGYCAATTYMTTTRAGTTT";
+                // Use specific primers based on target
+                let (primer_f, primer_r) = match target.to_lowercase().as_str() {
+                    "18s" => ("TTGTACACACCGCCC", "CCTTCYGCAGGTTCACCTAC"),
+                    "16s" => ("GTGYCAGCMGCCGCGGTAA", "CCGYCAATTYMTTTRAGTTT"),
+                    _ => return Err("Invalid target region".into()),
+                };
                 run_conda_qiime_command(env_name, &format!(
                     "feature-classifier extract-reads \
                      --i-sequences {} \