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Update README.md
Co-authored-by: Sofia Ochkalova <61541445+ochkalova@users.noreply.github.com>
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‎README.md‎

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@@ -169,17 +169,20 @@ See the [usage documentation](docs/usage.md#submission-study) for more details.
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### Data privacy
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You can use private data from ENA if you have access to it (you can login to Webin account and see the data). If you want to refer to private data you need to specify flag `--is_private`. Pipeline will use specified credentials to fetch metadata.
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You can reference private ENA data if you have access to it via your Webin account (it was submitted previously under your credentials). To use private data accessions in your submission metadata, specify the `--is_private` flag. The pipeline will then use your provided Webin credentials to fetch the required metadata.
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You can also keep submitted data private. If you already have a study and will pass it with `--submission_study` your submitted data will have the same privacy as your study. If you don't have a study then pipeline will register a new study for you. If you need that study being private you should specify **date** when it will become public with `--hold_data_private YYYY-MM-DD` (max 2 years from now).
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You can also control the privacy of your submitted data:
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| Example | Source of data | Submission data | Necessary arguments | Result |
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| -------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------- | --------------- | --------------------------------------------------------- | ------------------------------------------------------- |
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| Assemblies generated from public reads. Assemblies should be **public** right after submission | public | public | - | SUCCESS |
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| Assemblies generated from public reads. Assemblies should be private for 1 year after submission | public | private | `--hold_data_private today(YYYY-MM-DD)+1Y` | SUCCESS |
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| Bins generated from private reads and assemblies. Bins should be public after submission. User **has access** to reads and assemblies via Webin account | private | public | `--is_private` | SUCCESS |
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| Bins generated from private reads and assemblies. Bins should be private for 2 years after submission. User **has access** to reads and assemblies via Webin account | private | private | `--is_private`,`--hold_data_private today(YYYY-MM-DD)+2Y` | SUCCESS |
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| MAGs generated from private reads and assemblies. MAGs should be public after submission. User **does not have access** to reads and assemblies via Webin account | private | public | - | ERROR (submission should refer to only accessible data) |
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- If you provide an existing study via `--submission_study`, your submission will inherit the same privacy status as that study.
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- If no study is provided, the pipeline will register a new one for you. To keep this new study private, you must specify a release date using `--hold_data_private YYYY-MM-DD` (up to 2 years from the current date).
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| Example | Source Data | Submission Visibility | Required Arguments | Result |
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| -------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------- | --------------------- | -------------------------------------------------------- | ------------------------------------------------------- |
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| Assemblies generated from public reads. Assemblies should be public immediately after submission | public | public | – | SUCCESS |
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| Assemblies generated from public reads. Assemblies should remain private for 1 year after submission | public | private | `--hold_data_private today(YYYY-MM-DD)+1Y | SUCCESS |
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| Bins generated from private reads and assemblies. Bins should be public after submission. User **has access** to the reads and assemblies via Webin account | private | public | `--is_private` | SUCCESS |
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| Bins generated from private reads and assemblies. Bins should remain private for 2 years after submission. User **has access** via Webin account | private | private | `--is_private`, `--hold_data_private YYYY-MM-DD` (+2 years) | SUCCESS |
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| MAGs generated from private reads and assemblies. MAGs should be public after submission. User **does not have access** to the reads and assemblies via Webin account | private | public | – | ERROR (submission can only reference accessible data) |
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### Database setup (`CheckM2` and `CAT_pack`)
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