updated cli:

* Added clean_symlinks
* Design looks in more places for files

seqnado/cli.py

@@ -53,12 +53,31 @@ def cli_design(method, files, output="design.csv"):
     """
     import pathlib
     from seqnado.design import Design, DesignIP, FastqFile, FastqFileIP
-
+    from loguru import logger    
+
     if not files:
-        files = list(pathlib.Path(".").glob("*.fastq.gz"))
+        potential_file_locations = [
+            ".",
+            "fastqs",
+            "fastq",
+            "data",
+            "data/fastqs",
+        ]
+
+        for location in potential_file_locations:
+            files = list(pathlib.Path(location).glob("*.fastq.gz"))
+            if files:
+                break
 
         if not files:
-            raise ValueError("No fastq files provided or found in current directory.")
+            logger.error("No fastq files provided or found in current directory")
+            logger.error(f"""
+                         Fastq files can be provided as arguments or found in the following directories:
+                         {potential_file_locations}
+                         """)
+            raise ValueError("No fastq files provided or found in current directory" )
+
+
 
     if not method == "chip":
         design = Design.from_fastq_files([FastqFile(path=fq) for fq in files])
@@ -92,14 +111,19 @@ def cli_design(method, files, output="design.csv"):
             """,
     type=click.Choice(choices=["lc", "ls", "ss"]),
 )
+@click.option(
+    "--clean-symlinks",
+    is_flag=True,
+    help="Remove symlinks created by previous runs. Useful for re-running pipeline after misconfiguration.",
+)
 @click.argument("pipeline_options", nargs=-1, type=click.UNPROCESSED)
 def cli_pipeline(
     method,
     pipeline_options,
     help=False,
     preset="local",
     version=False,
-    apptainer_args="",
+    clean_symlinks=False,
 ):
     """Runs the data processing pipeline"""
 
@@ -116,6 +140,14 @@ def cli_pipeline(
 
     pipeline_options, cores = extract_cores_from_options(pipeline_options)
 
+    # Removes old symlinks if requested
+    if clean_symlinks:
+        logger.info("Cleaning symlinks")
+        links = pathlib.Path("seqnado_output/fastqs").glob("*")
+        for link in links:
+            if link.is_symlink():
+                link.unlink()
+
     cmd = [
         "snakemake",
         "-c",