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IKIM-Essen · Aug 26, 2024 · 2a836ab · 2a836ab
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diff --git a/docs/installation.md b/docs/installation.md
@@ -83,15 +83,17 @@ The structure can be adjusted via the config file: `config/config.yaml` under
   Defaults to `../archive/`.
 
 ### ONT sample preprocessing
-Automates the extraction of sequencing reads from sample-specific folders, merges the reads from each   barcode into a single FASTQ file, and then renames the files for easy identification and downstream analysis.
+Automates the extraction of sequencing reads from sample-specific folders, merges the reads from each 
+  barcode into a single FASTQ file, and then renames the files for easy identification and downstream analysis.
 
-- **barcode.csv**: A CSV file containing the barcode sequences and their corresponding sample    identifiers.
-- **source_dir**: The directory path where the barcode-specific folders are located.
-- **output_dir**: The directory path where the renamed FASTQ files will be saved. 
+- **barcode-rename.csv**: A CSV file containing the barcode sequences and their corresponding sample 
+  identifiers.
+- **barcode_dir**: The directory path where the barcode-specific folders are located.
+- **output_dir**: The directory path where the renamed FASTQ files will be saved.
 
 To run the tool, use the following command:
 ```sh
-snakemake --config source_dir=path/to/barcode/folders output_dir=data/date/ --cores all --use-conda barcode_rename
+  snakemake --config barcode_dir=path/to/barcode/folders output_dir=data/date/ --cores all --use-conda barcode_rename
 ```
 
 ### Sample sheet

diff --git a/workflow/rules/preprocessing.smk b/workflow/rules/preprocessing.smk
@@ -18,7 +18,7 @@ rule update_sample:
 rule barcode_rename:
     input:
         barcodes="barcode-rename.csv",
-        source_dir=config["source_dir"],
+        barcode_dir=config["barcode_dir"],
     output:
         out_dir=directory(config["output_dir"]),
     log:

diff --git a/workflow/scripts/barcode_rename.py b/workflow/scripts/barcode_rename.py
@@ -64,7 +64,7 @@ def rename_files(final_dir):
 config = snakemake.config
 
 barcode_csv = str(snakemake.input.barcodes)
-source_path = str(config["source_dir"])
+source_path = str(config["barcode_dir"])
 out_dir = str(config["output_dir"])
 
 if not os.path.exists(source_path):