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relecov-tools Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[1.2.0] - 2024-10-11 : https://github.com/BU-ISCIII/relecov-tools/releases/tag/1.2.0

Credits

Code contributions to the release:

Modules

  • Included wrapper module to launch download, read-lab-metadata and validate processes sequentially #322
  • Changed launch-pipeline name for pipeline-manager when tools are used via CLI #324

Added enhancements

  • Now also check for gzip file integrity after download. Moved cleaning process to end of workflow #313
  • Introduced a decorator in sftp_client.py to reconnect when conection is lost #313
  • Add Hospital Universitari Doctor Josep Trueta to laboratory_address.json [#316] (#316)
  • samples_data json file is no longer mandatory as input in read-lab-metadata #314
  • Included handling of alternative column names to support two distinct headers using the same schema in read-lab-metadata #314
  • Included a new hospital (Hospital Universitario Araba) to laboratory_address.json #315
  • More accurate cleaning process, skipping only sequencing files instead of whole folder #321
  • Now single logs summaries are also created for each folder during download #321
  • Introduced handling for missing/dup files and more accurate information in prompt for pipeline_manager #321
  • Included excel resize, brackets removal in messages and handled exceptions in log_summary.py #322
  • Included processed batchs and samples in read-bioinfo-metadata log summary #324
  • When no samples_data.json is given, read-lab-metadata now creates a new one #324
  • Handling for missing sample ids in read-lab-metadata #324
  • Better logging for download, read-lab-metadata and wrapper #324

Fixes

  • Fixed wrong city name in relecov_tools/conf/laboratory_address.json #320
  • Fixed wrong single-paired layout detection in metadata due to Capital letters #321
  • Error handling in merge_logs() and create_logs_excel() methods for log_summary.py #322
  • Included handling of multiple empty rows in metadata xlsx file #322

Changed

  • Renamed and refactored "bioinfo_lab_heading" for "alt_header_equivalences" in configuration.json #314
  • Included a few schema fields that were missing or outdated, related to bioinformatics results #314
  • Updated metadata excel template, moved to relecov_tools/assets #320
  • Now python lint only triggers when PR includes python files #320
  • Moved concurrency to whole workflow instead of each step in test_sftp-handle.yml #320
  • Updated test_sftp-handle.yml testing datasets #320
  • Now download skips folders containing "invalid_samples" in its name #321
  • read-lab-metadata: Some warnings now include label. Also removed trailing spaces #322
  • Renamed launch-pipeline for pipeline-manager and updated keys in configuration.json #324
  • Pipeline manager now splits data based on enrichment_panel and version. One folder for each group #324

Removed

  • Removed duplicated tests with pushes after PR was merged in test_sftp-handle #312
  • Deleted deprecated auto-release in pypi_publish as it does not work with tag pushes anymore #312
  • Removed first sleep time for reconnection decorator in sftp_client.py, sleep time now increases in the second attempt #321

Requirements

[1.1.0] - 2024-09-13 : https://github.com/BU-ISCIII/relecov-tools/releases/tag/1.1.0

Credits

Code contributions to the release:

Modules

  • New logs-to-excel function to create an excel file given a list of log-summary.json files #300

Added enhancements

  • Included a way to extract pango-designation version in read-bioinfo-metadata #299
  • Now log_summary.py also creates an excel file with the process logs #300
  • Read-bioinfo-metadata splits files and data by batch of samples #306
  • Included a sleep time in test_sftp-handle to avoid concurrency check failure #308

Fixes

  • Fixes in launch_pipeline including creation of samples_id.txt and joined validated json #303
  • Fixed failing module_tests.yml workflow due to deprecated upload-artifact version #308

Changed

  • Changed pypi_publish action to publish on every release, no need to push tags #308

Removed

  • Removed only_samples argument in log_summary.py as it was not used in any module. #300

Requirements

[1.0.0] - 2024-09-02 : https://github.com/BU-ISCIII/relecov-tools/releases/tag/1.0.0

Credits

Code contributions to the inital release: