-`./spsp auto`- Automatically run the commands to Compress$, Hash, Encrypt & Transfer, add --no-archive option to delete the files after the transfer\ the sent files
-`./spsp compress <folder>` - compress a folder to tar.gz archive
-`./spsp help` - Shows help screen
-`./spsp encrypt <file>` - encrypts a file using gpg command and SPSP public key (which needs to be in your own GPG keys list)
-`./spsp test` - Dry run with fake generated files with report
-`./spsp hash <file>` - generates the hash of a file using SHA-256 algorithm
-`./spsp cleanup` - Clean the following directories: logs, sent, viruses, bacteria and .outbox
-`./spsp transfer <file>` - transfers a file through sftp to SPSP server (your SSH key needs to be validated by SPSP to use this command)
-`./spsp auto`- automatically run the transfer-tool (this needs to be combined with a CRON task, see below for more information), add `--no-archive` or `-NA` to not keep the sent files
-`./spsp help` - displays the help
## How to prepare FASTQ files with the metadata file
## How to prepare FASTQ files with the metadata file