Minor changes for easy running with conda

Author: pgangwar-ucsd

Snakefile

@@ -103,8 +103,6 @@ def check_input_files():
         if len(r1_files) != 1 or len(r2_files) != 1: raise RuntimeError("Paired-end requires exactly one *_R1.fastq and *_R2.fastq")
         fq1 = str(gzip_if_needed(r1_files[0]))
         fq2 = str(gzip_if_needed(r2_files[0]))
-
-    print(f"Input FASTQs chosen:\n  FQ1 = {fq1}\n  FQ2 = {fq2}", file=sys.stderr)
     return fq1, fq2
 
 if not RUNNING_TEST:

scripts/add_ref_mat.py

@@ -496,7 +496,7 @@ def main():
     if not any_mat_available(ROOT_PATHOGENS_DIR):
         print(
             "\n\n[WARN] No MAT (.pb/.pb.gz) found in data/pathogens_for_wepp. "
-            "At least one pathogen with a MAT is required for the pipeline to run."
+            "At least one pathogen with a MAT is required for the pipeline to run.\n\n"
         )
     else:
         print("\n[INFO] Setup complete. Pathogen data is ready.")

scripts/kraken_data_visualization.py

@@ -5,6 +5,7 @@
 import os
 import math
 import subprocess
+from pathlib import Path
 
 # Usage:
 # python kraken_data_visualization.py <path_to_kraken_report_file> <visualization_file> 
@@ -208,7 +209,9 @@ def wrap_labels(labels, width=25):
 
 if add_species_runtime:
     # Call add_ref_mat.py to update the database
+    current_script_dir = Path(__file__).resolve().parent
+    add_ref_script = current_script_dir / "add_ref_mat.py"
     subprocess.run(
-                ["python", "scripts/add_ref_mat.py"],
+                [sys.executable, str(add_ref_script)],
                 check=True
             )