Ena-upload-cli

**Implemented enhancements:**

- Supporting all optional fields in the run/experiment and study xml [\37](https://github.com/usegalaxy-eu/ena-upload-cli/issues/37)

**Closed issues:**

- Empty rows give error [\52](https://github.com/usegalaxy-eu/ena-upload-cli/issues/52)
- Support FTPS connection to protect account credidentials [\48](https://github.com/usegalaxy-eu/ena-upload-cli/issues/48)
- Add GitHub Action to check if new xsd templates are added to ENA [\14](https://github.com/usegalaxy-eu/ena-upload-cli/issues/14)

**Merged pull requests:**

- FTPS stability and speed improvements [\55](https://github.com/usegalaxy-eu/ena-upload-cli/pull/55) ([bedroesb](https://github.com/bedroesb))
- Drop empty rows [\54](https://github.com/usegalaxy-eu/ena-upload-cli/pull/54) ([bedroesb](https://github.com/bedroesb))
- Updating introduction [\51](https://github.com/usegalaxy-eu/ena-upload-cli/pull/51) ([bedroesb](https://github.com/bedroesb))
- Correct use of optional attributes in run/experiment and study tables [\46](https://github.com/usegalaxy-eu/ena-upload-cli/pull/46) ([bedroesb](https://github.com/bedroesb))

**Implemented enhancements:**

- Changing release date through API [\36](https://github.com/usegalaxy-eu/ena-upload-cli/issues/36)
- If table is given without action values, an error is thrown [\34](https://github.com/usegalaxy-eu/ena-upload-cli/issues/34)

**Merged pull requests:**

- Adding TLS to the ftp connection [\50](https://github.com/usegalaxy-eu/ena-upload-cli/pull/50) ([bedroesb](https://github.com/bedroesb))
- Create CITATION.cff [\49](https://github.com/usegalaxy-eu/ena-upload-cli/pull/49) ([bedroesb](https://github.com/bedroesb))
- Adding release and cancel as an action [\41](https://github.com/usegalaxy-eu/ena-upload-cli/pull/41) ([bedroesb](https://github.com/bedroesb))

**Implemented enhancements:**

- Adding flag to not do a submission but just to generate the XMLs [\43](https://github.com/usegalaxy-eu/ena-upload-cli/issues/43)
- If table is given without action values, an error is thrown [\34](https://github.com/usegalaxy-eu/ena-upload-cli/issues/34)

**Merged pull requests:**

- Handling tables that have no actions in the status column [\45](https://github.com/usegalaxy-eu/ena-upload-cli/pull/45) ([bedroesb](https://github.com/bedroesb))
- Adding draft flag to not perform a submission [\44](https://github.com/usegalaxy-eu/ena-upload-cli/pull/44) ([bedroesb](https://github.com/bedroesb))
- Automatic update of ENA Sample Checklists [\42](https://github.com/usegalaxy-eu/ena-upload-cli/pull/42) ([github-actions[bot]](https://github.com/apps/github-actions))

**Merged pull requests:**

- Adding back tool name to sample metadata [\39](https://github.com/usegalaxy-eu/ena-upload-cli/pull/39) ([bedroesb](https://github.com/bedroesb))

This new version includes especially bug fixes.

**Fixed bugs:**

- --no\_upload parameter not working [\33](https://github.com/usegalaxy-eu/ena-upload-cli/issues/33)
- Most minimal example not working [\29](https://github.com/usegalaxy-eu/ena-upload-cli/issues/29)

**Closed issues:**

- Possible values for file\_format are not clear [\30](https://github.com/usegalaxy-eu/ena-upload-cli/issues/30)

**Merged pull requests:**

- Generating md5 hash when not given with -no\_upload flag [\35](https://github.com/usegalaxy-eu/ena-upload-cli/pull/35) ([bedroesb](https://github.com/bedroesb))
- Updating documentation about modify [\32](https://github.com/usegalaxy-eu/ena-upload-cli/pull/32) ([bedroesb](https://github.com/bedroesb))
- Fixing template to allow no filled in optional fields [\31](https://github.com/usegalaxy-eu/ena-upload-cli/pull/31) ([bedroesb](https://github.com/bedroesb))
- Fixing bug if empty cell for file\_checksum column [\28](https://github.com/usegalaxy-eu/ena-upload-cli/pull/28) ([bedroesb](https://github.com/bedroesb))

IMPORTANT: the `no_upload` flag is changed to a more understanding flag: `--no_data_upload`

**Implemented enhancements:**

- Dropping unnecessary columns [\21](https://github.com/usegalaxy-eu/ena-upload-cli/issues/21)
- Adding support for all official ENA checklists [\20](https://github.com/usegalaxy-eu/ena-upload-cli/issues/20)
- Possibility to give the taxon\_id through the table [\6](https://github.com/usegalaxy-eu/ena-upload-cli/issues/6)

**Closed issues:**

- Library name generation [\23](https://github.com/usegalaxy-eu/ena-upload-cli/issues/23)

**Merged pull requests:**

- Taxon ID parsing improvements [\27](https://github.com/usegalaxy-eu/ena-upload-cli/pull/27) ([bedroesb](https://github.com/bedroesb))
- Adding support for all official sample checklists on ENA [\26](https://github.com/usegalaxy-eu/ena-upload-cli/pull/26) ([bedroesb](https://github.com/bedroesb))
- Taking away the need to give columns that are automatically filled in by the tool [\25](https://github.com/usegalaxy-eu/ena-upload-cli/pull/25) ([bedroesb](https://github.com/bedroesb))
- Allow to skip file upload and provide a file of filenames as source for data files [\24](https://github.com/usegalaxy-eu/ena-upload-cli/pull/24) ([mobilegenome](https://github.com/mobilegenome))
- Adding support for multiple checklists [\19](https://github.com/usegalaxy-eu/ena-upload-cli/pull/19) ([bedroesb](https://github.com/bedroesb))
- Read md5sum from table, and only generate if missing [\18](https://github.com/usegalaxy-eu/ena-upload-cli/pull/18) ([mobilegenome](https://github.com/mobilegenome))
- Add ENA\_template\_ERC000011\_sample.xml [\17](https://github.com/usegalaxy-eu/ena-upload-cli/pull/17) ([rabuono](https://github.com/rabuono))
- Small fixes based on \15 [\16](https://github.com/usegalaxy-eu/ena-upload-cli/pull/16) ([bedroesb](https://github.com/bedroesb))


**NOTE: This release is not backwards compatible with previous release! Check following things if you update from 0.3.1 or earlier:**
- Headers in the sample table will now follow the exact vocabulary as on [ENA](https://www.ebi.ac.uk/ena/browser/checklists)
- The `--vir` parameter is not supported anymore and is replaced by `--checklist ERC000033` + support for all official checklists
- The *scientific_name* column in the sample table is not mandatory anymore + the *taxon_id* column is recommended instead
- Sample columns *accession*,*submission_date*, *status* are not needed anymore