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To save reports directly in an S3 bucket, use: -B/--output-bucket. 
prowler aws -B my-bucket

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Custom Folder and Filename

For a custom folder and/or filename, specify: -o/--output-directory and/or -F/--output-filename. 
prowler aws \
        -B my-bucket \
        --output-directory test-folder \
        --output-filename output-filename

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Custom Output Formats

By default, Prowler sends HTML, JSON, and CSV output formats. To specify a single output format, use the -M/--output-modes flag. 
prowler aws -M csv -B my-bucket
If you prefer using the initial credentials instead of the assumed role credentials for uploading reports, use -D/--output-bucket-no-assume instead of -B/--output-bucket.
Ensure the credentials used have write permissions for the s3:PutObject where reports will be uploaded.