Merge pull request #74 from nf-core/dev

Release 2.0.0

CHANGELOG.md

@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [v2.0.0](https://github.com/nf-core/metaboigniter/releases/tag/2.0.0) - 2023-12-05
+## [v2.0.0](https://github.com/nf-core/metaboigniter/releases/tag/2.0.0) - 2023-12-18
 
 Initial release of DSL 2 version nf-core/metaboigniter including major modifications.
 The support for the previous parameters in version 1.0.1 has been deprecated.

bin/cleanup.py

@@ -60,7 +60,7 @@ def modify_tsv_column(input_file, output_file, old_column_name, new_column_name,
         for row in reader:
             # Rearrange the row data based on new headers
             value_to_move = row.pop(old_position)
-            value_to_move.replace("e_", "")
+            value_to_move = value_to_move.replace("e_", "")
             row.insert(new_position, value_to_move)
 
             writer.writerow(row)

bin/download_models.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+
+# Check if correct number of arguments are provided
+if [ "$#" -ne 2 ]; then
+    echo "Usage: $0 filename.csv output_folder"
+    exit 1
+fi
+
+# File containing URLs
+CSV_FILE="$1"
+
+# Directory where files will be downloaded
+DOWNLOAD_DIR="$2"
+
+# Create the directory if it doesn't exist
+mkdir -p "$DOWNLOAD_DIR"
+
+# Skip the first line (header) and read each subsequent line from the CSV file
+tail -n +2 "$CSV_FILE" | while IFS= read -r url
+do
+    # Download the file using wget or curl
+    wget -P "$DOWNLOAD_DIR" "$url" || curl -o "${DOWNLOAD_DIR}/$(basename $url)" "$url"
+done