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- `./spsp test` - Dry run with fake generated files with report
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- `./spsp cleanup` - Clean the following directories: logs, sent, viruses, bacteria, and .outbox
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## How to prepare FASTQ files with the metadata file
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## How to prepare your data for submission
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This step assumes that you already followed the guide on [spsp.ch](https://spsp.ch/) and will only tell you how you should organize your files for the Transfer Tool to work properly:
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- Start by **identifying** if your sequences are from **viruses** or **bacteria** (if mixed, you need to separate them)
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- Make sure that the sequences described in your metadata file **match** the FASTQ files
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- Start by **identifying** if your sequences are from **viruses** or **bacteria** (if mixed, please separate them)
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- **Create a subfolder** as the date of the day (for example: 26-06-12) **inside bacteria/viruses directory** depending on their type
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- **COPY** your FASTQ files and the corresponding metadata file inside the freshly created folder
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- **COPY** your metadata file and any associated sequencing data (FASTA, FASTQ, BAM, CRAM) inside the freshly created folder
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**IT IS VERY IMPORTANT TO ALWAYS PUT YOUR FASTQ FILES AND METADATA FILE INSIDE A SUBFOLDER IN THE BACTERIA/VIRUSES DIRECTORY, OR THE TT WILL IGNORE THE FILES**
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**IT IS VERY IMPORTANT TO ALWAYS PUT YOUR DATA INSIDE A SUBFOLDER IN THE BACTERIA/VIRUSES DIRECTORY, OR THE TT WILL IGNORE THE FILES**
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## How to transfer files easily
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If you want to quickly and easily send a batch of FASTQ files with their metadata, just follow those instructions:
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If you want to quickly and easily send a batch of data, just follow those instructions:
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- Follow the instructions on [How to prepare FASTQ files with the metadata file](#how-to-prepare-fastq-files-with-the-metadata-file)
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- Follow the instructions on [How to prepare your data for submission](#how-to-prepare-your-data-for-submission)
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- Launch the pipeline by typing `./spsp auto` which will trigger the **automatic** mode
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- Once the transfer is over, you should find the sent files (encrypted archive and hash file) in the `sent` folder
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