Pull request overview

This PR fixes an alignment directory issue by changing how the alignment file path is determined. Instead of passing the input parameter directly to GetAlignmentFileBean, it now extracts the directory path from the first analysis file and validates both the analysis files collection and directory existence.

Key changes:

• Added validation to check if analysis files list is empty before processing
• Added directory existence check for the alignment folder
• Changed alignment file parsing to use the directory from the first analysis file instead of the input parameter

            if (analysisFiles.IsEmptyOrNull()) {
                Console.WriteLine(CommonProcess.NoFileError());
                return false;
            }

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