Credits
Code contributions to the release:
- [Juan Ledesma](https://github.com/juanledesma78)
- [Pablo Mata](https://github.com/Shettland)
- [Sergio Olmos](https://github.com/OPSergio)
Modules
- Included wrapper module to launch download, read-lab-metadata and validate processes sequentially [322](https://github.com/BU-ISCIII/relecov-tools/pull/322)
- Changed launch-pipeline name for pipeline-manager when tools are used via CLI [324](https://github.com/BU-ISCIII/relecov-tools/pull/324)
Added enhancements
- Now also check for gzip file integrity after download. Moved cleaning process to end of workflow [313](https://github.com/BU-ISCIII/relecov-tools/pull/313)
- Introduced a decorator in sftp_client.py to reconnect when conection is lost [313](https://github.com/BU-ISCIII/relecov-tools/pull/313)
- Add Hospital Universitari Doctor Josep Trueta to laboratory_address.json [316] (https://github.com/BU-ISCIII/relecov-tools/pull/316)
- samples_data json file is no longer mandatory as input in read-lab-metadata [314](https://github.com/BU-ISCIII/relecov-tools/pull/314)
- Included handling of alternative column names to support two distinct headers using the same schema in read-lab-metadata [314](https://github.com/BU-ISCIII/relecov-tools/pull/314)
- Included a new hospital (Hospital Universitario Araba) to laboratory_address.json [315](https://github.com/BU-ISCIII/relecov-tools/pull/315)
- More accurate cleaning process, skipping only sequencing files instead of whole folder [321](https://github.com/BU-ISCIII/relecov-tools/pull/321)
- Now single logs summaries are also created for each folder during download [321](https://github.com/BU-ISCIII/relecov-tools/pull/321)
- Introduced handling for missing/dup files and more accurate information in prompt for pipeline_manager [321](https://github.com/BU-ISCIII/relecov-tools/pull/321)
- Included excel resize, brackets removal in messages and handled exceptions in log_summary.py [322](https://github.com/BU-ISCIII/relecov-tools/pull/322)
- Included processed batchs and samples in read-bioinfo-metadata log summary [324](https://github.com/BU-ISCIII/relecov-tools/pull/324)
- When no samples_data.json is given, read-lab-metadata now creates a new one [324](https://github.com/BU-ISCIII/relecov-tools/pull/324)
- Handling for missing sample ids in read-lab-metadata [324](https://github.com/BU-ISCIII/relecov-tools/pull/324)
- Better logging for download, read-lab-metadata and wrapper [324](https://github.com/BU-ISCIII/relecov-tools/pull/324)
Fixes
- Fixed wrong city name in relecov_tools/conf/laboratory_address.json [320](https://github.com/BU-ISCIII/relecov-tools/pull/320)
- Fixed wrong single-paired layout detection in metadata due to Capital letters [321](https://github.com/BU-ISCIII/relecov-tools/pull/321)
- Error handling in merge_logs() and create_logs_excel() methods for log_summary.py [322](https://github.com/BU-ISCIII/relecov-tools/pull/322)
- Included handling of multiple empty rows in metadata xlsx file [322](https://github.com/BU-ISCIII/relecov-tools/pull/322)
Changed
- Renamed and refactored "bioinfo_lab_heading" for "alt_header_equivalences" in configuration.json [314](https://github.com/BU-ISCIII/relecov-tools/pull/314)
- Included a few schema fields that were missing or outdated, related to bioinformatics results [314](https://github.com/BU-ISCIII/relecov-tools/pull/314)
- Updated metadata excel template, moved to relecov_tools/assets [320](https://github.com/BU-ISCIII/relecov-tools/pull/320)
- Now python lint only triggers when PR includes python files [320](https://github.com/BU-ISCIII/relecov-tools/pull/320)
- Moved concurrency to whole workflow instead of each step in test_sftp-handle.yml [320](https://github.com/BU-ISCIII/relecov-tools/pull/320)
- Updated test_sftp-handle.yml testing datasets [320](https://github.com/BU-ISCIII/relecov-tools/pull/320)
- Now download skips folders containing "invalid_samples" in its name [321](https://github.com/BU-ISCIII/relecov-tools/pull/321)
- read-lab-metadata: Some warnings now include label. Also removed trailing spaces [322](https://github.com/BU-ISCIII/relecov-tools/pull/322)
- Renamed launch-pipeline for pipeline-manager and updated keys in configuration.json [324](https://github.com/BU-ISCIII/relecov-tools/pull/324)
- Pipeline manager now splits data based on enrichment_panel and version. One folder for each group [324](https://github.com/BU-ISCIII/relecov-tools/pull/324)
Removed
- Removed duplicated tests with pushes after PR was merged in test_sftp-handle [312](https://github.com/BU-ISCIII/relecov-tools/pull/312)
- Deleted deprecated auto-release in pypi_publish as it does not work with tag pushes anymore [312](https://github.com/BU-ISCIII/relecov-tools/pull/312)
- Removed first sleep time for reconnection decorator in sftp_client.py, sleep time now increases in the second attempt [321](https://github.com/BU-ISCIII/relecov-tools/pull/321)
Requirements