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CHANGELOG.md

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Changelog

dev

Added

  • "mergereads" task for merging forward and reverse reads using PEAR (#121)

Changed

  • Reorganized Box client and updated auth URL to search for in server logs when authenticating with OAuth (#120)

0.0.5 - 2021-01-19

Added

  • error property for illumina.alignment.Alignment class (#104)
  • BCL stats file parsing functions for applicable Illumina runs (#106)

Changed

  • Use faster re-tries for small file uploads to Box (#111)
  • Use fully-resolved paths for alignment directory tracking in Run.refresh (#111)
  • Reorganize unit tests for speed and simplicity (#111)

Fixed

  • Only process an alignment when its containing run is marked complete (#108)
  • Handle non-unicode characters in CSV files (#105, #115)

0.0.4 - 2020-09-08

Added

  • Unit tests for each individual task class (#99)

Changed

  • Always read task names as lowercase when parsing metadata.csv files (#95)
  • Parse fastq.gz files per sample from disk rather than predicting from sample name alone (#94)

Fixed

  • Correct parsing of contig numbers in task_assemble to include all digits (#100)
  • Correct parsing for Illumina's Checkpoint.txt files to work with incomplete alignment outputs (#97)

0.0.3 - 2020-08-19

Added

  • --version argument to command-line interface (#87)

Changed

  • Use Unix-style line endings in report CSV (#86)
  • Suppress duplicate log messages for skipped runs (#85)

Fixed

  • Suppress excessive logging for Box file uploads (#89)
  • Specify minimum versions for dependencies during install (#84)

0.0.2 - 2020-08-04

Added

  • Support for custom task classes (#56)
  • Timeout feature for manual and geneious tasks (#66)
  • Flow cell ID property for Illumina run objects (#75)

Changed

  • Append flow cell ID from each run to project workdir names (#76)
  • Ignore empty rows and columns when parsing metadata.csv files (#73)
  • Use chunked Box.com uploader for more reliable uploads of large files (#69)
  • Handle missing Experiment Name in sample sheets (#59)

Fixed

  • Catch and log errors parsing metadata.csv files during project setup (#74)
  • Handle missing FASTQ file case during project setup (#63)

0.0.1 - 2019-06-03

First named release