v2.0.2: Clean-up

What's Changed

Improvements

• Write script to access Applied method field in old releases in scripts folder with helper scripts by @marinak-ebi in #81
• Write script run_pipeline.sh that run both statistical and annotation pipeline by @marinak-ebi in #85
• Recreate conda environment from scratch by @marinak-ebi in #82

Docs

• Update LICENSE copyright owner by @marinak-ebi in #86

Refactor

• Remove the statistical pipeline unused code by @marinak-ebi in #87
• Get rid of EquationMap.conf and functions that process this file by @marinak-ebi in #89

Full Changelog: v2.0.1...v2.0.2

This version of the pipeline was used in DR22.0

v2.0.1 | EYE data bug fix

Bug fixes

• Update mapping files for ocular phenotypes to fix error during eye data analysis by @marinak-ebi in #78

Full Changelog: v2.0.0...v2.0.1

This version of the pipeline was used in DR21.1

v2.0.0 | SLURM pipeline

Bug fixes

• Fix error during gross morphology data analysis by @marinak-ebi in #65
• Fix logs of annotation pipeline by @marinak-ebi in #67
• Update CategoryMap.conf for renaming eye morphology categories by @marinak-ebi in #70

Refactor

• Migrate all pipelines from LSF to SLURM by @marinak-ebi in #63
• Create function submit_limit_jobs that limit number of submitted job by @marinak-ebi in #64
• Streamline mp_chooser file naming by @marinak-ebi in #68
• Refactor how mp_chooser file is specified by @marinak-ebi in #72
• Update instructions for running on SLURM by @marinak-ebi in #73

Full Changelog: v1.0.0...v2.0.0

This version of the pipeline was used in DR21.0

v1.0.0 | Stable LSF pipeline

Bug fixes

• Keep all logs in separate files by @marinak-ebi in #36
• Fix errors during log file generation by @marinak-ebi in #39
• Remove multicore initialisation and address serverSocket error by @marinak-ebi in #47

Improvements

• Refactor dependency installation by @marinak-ebi in #35
• Parameterise UpdatePackagesFromGithub.R by @marinak-ebi in #40

Docs

• Unify running instructions by @marinak-ebi in #33
• Update LSF running instructions by @marinak-ebi in #53

Clean up

• Remove Early adults stats pipeline directory by @marinak-ebi in #19
• Remove all PhenStat mentions by @marinak-ebi in #20
• Clean up OpenStats by @marinak-ebi in #21
• Remove IMPC Pain WG directory by @marinak-ebi in #24
• Remove MiniAnalyses directory by @marinak-ebi in #26
• Remove Other projects directory by @marinak-ebi in #27
• Remove Docker mentions by @marinak-ebi in #28

Full Changelog: baseline...v1.0.0