1.8.0

Added

• Add JSON and HTML reports to archived files
• Add BAM indices (bai) to archived files

Changed

• Include archive creation script in automatic release
• Add default ignored directories 'Install_logs' and 'persistence'

1.7.0

Added

• Remove run directories after a delay, if they are empty
• Automated GitHub release on tagging
• Add iRODS 4.2.11 to GitHub Actions workflow

Changed

• Bump github.com/onsi/ginkgo from 1.16.5 to 2.1.4
• Bump github.com/onsi/gomega from 1.17.0 to 1.19.0
• Bump github.com/stretchr/testify from 1.7.0 to 1.7.1
• Bump github.com/spf13/cobra from 1.2.1 to 1.4.0

1.6.0

Added

• Support for adding iRODS metadata for PromethION-24 runs.
• Support for BAM files.
• Support for BED files (compressed).
• iRODS 4.2.10 support.

Changed

• Build with Go.1.17

• Bump github.com/rs/zerolog from 1.21.0 to 1.26.1

• Bump github.com/onsi/ginkgo from 1.16.2 to 1.16.5

• Bump github.com/onsi/gomega from 1.11.0 to 1.17.0

• Bump github.com/spf13/cobra from 0.0.7 to 1.3.0

Removed

• Travis CI configuration.
• PromethION beta report parsing tests and unused test data.

1.5.0

Added

• Add Github Actions test workflow
• Improve recognition of files to be processed and archived
• Add support for TSV files.
• Add support for compressing CSV files.
• Add new all ONT-specific paths to the exclusion list.
• Add the /data/laboratory WSI-specific path to the exclusion list.
• Add iRODS 4.2.8 support

Removed

• Remove iRODS 4.1.12 support

Changed

• Relocate repository from github.com/kjsanger to github.com/wtsi-npg

• Bump github.com/wtsi-npg/extendo/v2 from 2.2.0 to 2.4.0

• Bump github.com/wtsi-npg/logshim from to 1.1.0 to 1.3.0

• Bump github.com/wtsi-npg/logshim-zerolog from 1.1.0 to 1.3.0

• Bump github.com/klauspost/pgzip from 1.2.1 to 1.2.5

• Bump github.com/onsi/ginkgo from 1.12.3 to 1.16.1

• Bump github.com/onsi/gomega from 1.10.1 to 1.11.0

• Bump github.com/rs/zerolog from 1.19.1 to 1.21.0

• Bump github.com/spf13/cobra from 0.0.5 to 0.0.7

1.4.0

Added

• PromethION support for enhanced metadata.
• iRODS 4.2.7 clients to the test matrix.
• "ont" namespace to iRODS metadata attributes.

Changed

• Bump github.com/kjsanger/extendo from 2.1.0 to 2.2.0

1.3.0

Added

• Add experiment_name and instrument_slot to report metadata.

Changed

• Bump github.com/stretchr/testify from 1.5.1 to 1.6.0
• Bump github.com/onsi/ginkgo from 1.12.0 to 1.12.2

1.2.0

Added

• A systemd unit template and wrapper script.
• A String() method for WorkPlan.
• Logging immediately before and after a work function is called.

Changed

• Improved verbose level logging for consistency and information.

• Added to default paths to ignore in the data root.

• Bump github.com/kjsanger/extendo from 1.1.0 to 2.0.0

• Bump github.com/onsi/ginkgo from 1.10.3 to 1.12.0

• Bump github.com/onsi/gomega from 1.7.1 to 1.9.0

Fixed

• Hang or failure to exit cleanly when encountering errors, such as
  unreadable directories.
• Hang on cancel when data root does not exist.
• Exclude TMPDIR from archiving.
• A --version CLI option.

1.1.0

Added

• Checksum creation improvements using tee'ing to avoid re-reading data.
• Make the size of the client pool equal to the number of threads.
• Use pgzip implementation.
• Gzip compression of fastq and txt files.
• Enhancements to FilePath for handling compressed files.
• Find paths immediately, then at intervals.

Changed

• Bump github.com/kjsanger/extendo from 1.0.0 to 1.1.0
• Bump github.com/onsi/gomega from 1.5.0 to 1.7.1
• Bump github.com/onsi/ginkgo from 1.8.0 to 1.10.3
• Bump github.com/rs/zerolog from 1.14.3 to 1.17.2
• Bump github.com/stretchr/testify from 1.3.0 to 1.4.0

Fixed

• Check the error returned by ProcessFiles.
• Improvements to error handling in ProcessFiles.
• Allow cancellation of work to cause ProcessFiles to return.
• Compress files into a temporary location.