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CHANGELOG.md

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Changelog for EGCG-Project-Management

0.13 (unreleased)

  • Nothing changed yet.

0.12.0 (2019-10-08)

  • Cleaned up reference_data.upload_species_without_genome
  • report_runs now only reports the latest run in instances where a flowcell has been sequenced more than once
  • Fixes unexpected deletion of non-production runs in data_deletion.raw_data

0.11.1 (2019-08-08)

  • Bugfix for data download confirmation
  • Support for Asana API changes

0.11 (2019-07-29)

  • Project report updates:
    • KAPA library prep
    • GATK4 pipelines
    • Dragen rapid processing

0.10.1 (2019-04-29)

  • Removed old project report
  • Removed old aggregation usage
  • Pointing user to attached project report in delivery email

0.10 (2019-02-28)

  • Project report appendix tables are now fit dynamically, depending on their content
  • Project report code refactor, modifying project_information.py, project_report_latex.py, pylatex_ext.py and utils.py
  • Fixed bug when performing final data deletion by filtering out "Undetermined" sample IDs
  • Project report now supports different analysis types
  • Data deletion now removes sample folder
  • Provides more accurate feedback if data deletion fails, detailing only the cause of failure
  • Project report is now generated using Latex and converting it to PDF before exporting
  • lims.get_processes now uses the appropriate parameter
  • Try/except catches cases where human has more than one analysis type

0.9 (2018-11-30)

  • reference_data.py now downloads reference genomes from Ensembl and EnsemblGenomes. It also prepare the data, upload metadata and perform simple validation.
  • delete_data.py has a new mode for deletion of orphan filestub in the DMF filesystem
  • Fix bug in data deletion where fluidX samples where ignored in the delivered folder
  • New report run script that generate email to report successes/failures/repeats to the lab

0.8 (2018-08-08)

  • New mode in delete_data.py to perform final data deletion.
  • detect_sample_to_delete.py has a mode to detect sample ready for final deletion
  • Raw data deletion now select run that have been reviewed 14 days ago. It also uses notification in case of a crash

0.7 (2018-05-08)

  • Added customer details and signatures to project report (new config entry)
  • Added additional reporting to GeL data delivery and enhancing --force option
  • Switched data delivery over to use a delivery step URI
    • removed --mark_only, --project_id, --sample_id
    • added --process_id
  • Added integration test suite

0.6 (2018-01-17)

  • email sent in HTML rather than plain text
  • Project summary examples generated
  • Fixes made to project report

0.5 (2017-11-28)

  • Added new script to rsync data to GEL and notify their REST API
  • Added recall_sample.py for recalling a sample from tape

0.4 (2017-10-23)

  • Confirm delivery scripts added
  • Bug fix project report to use only samples that have been delivered

0.3 (2017-06-22)

  • Added reference_data for locating and documenting sources of reference genomes and variant databases
  • Updated EGCG-Core to v0.7.1
  • Added FluidX barcode support and email reporting to data delivery

0.2.4 (2017-03-30)

  • Fixed a bug where multiple non-human species in a project would crash project_report

0.2.3 (2017-03-27)

  • Refactor of automatic review and data deletion
  • Update data deletion to use Archive management from EGCG-Core

0.2.2 (2017-01-18)

0.2.1b (2016-11-29)

0.2.1a (2016-08-29)

0.2.1 (2016-08-26)

0.2 (2016-08-26)

This version adds a script to generate the project report.

0.1 (2016-07-28)