Version 0.0.5

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)

Version 0.0.4

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)

Version 0.0.3

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)

Version 0.0.2

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)