Feature request: Add Support for More File Formats (e.g., CRAM Instead of Just BAM)

[berntpopp]

Description: Extend the pipeline to support additional file formats, such as CRAM, to increase flexibility and compatibility with various input data sources.

Tasks:

• Add support for reading and processing CRAM files in addition to BAM files.
• Update input validation to detect and handle CRAM files.
• Modify any steps that assume BAM format to work with CRAM as well.
• Update documentation to reflect support for new file formats.

Example Code Block:

def process_alignment(input_file, output_dir, file_format="bam"):
    if file_format == "bam":
        return process_bam(input_file, output_dir)
    elif file_format == "cram":
        return process_cram(input_file, output_dir)
    else:
        raise ValueError(f"Unsupported file format: {file_format}")