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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased] - Unit tests

Added

Changed

  • Update valet_archive_create script to remove reference to conda
  • Update CI to use ubuntu latest
  • Update github actions test workflow baton to 4.0.0

Removed

  • Remove irods 4.2.10 from github actions test workflow

[1.8.0] - 2022-06-20

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] - 2022-05-19

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] - 2022-01-10

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] - 2021-04-15

Added

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

Removed

  • RODS 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] - 2020-09-14

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/wtsi-npg/extendo from 2.1.0 to 2.2.0

[1.3.0] - 2020-06-02

Added

  • experiment_name and instrument_slot to report metadata.

Changed

  • Bump github.com/wtsi-npg/extendo from 2.0.0 to 2.1.0
  • 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] - 2020-02-28

Added

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

Changed

  • Improve verbose level logging for consistency and information.

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

  • Bump github.com/wtsi-npg/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] - 2019-12-05

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.
  • Gzip compression of fastq and txt files.
  • Enhancements to FilePath for handling compressed files.
  • Find paths immediately, then at intervals.

Changed

  • Use pgzip implementation.

  • Bump github.com/wtsi-npg/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.

[1.0.0] - 2019-10-14

Added

  • Limit the absolute maximum number of threads to 12.
  • A --delete-on-archive CLI option to valet archive.
  • A valet archive command to move files to iRODS using extendo.
  • Support for dispatching to multiple different work functions.
  • A --dry-run CLI option to valet checksum.
  • Watch and sweep tree pruning capability.
  • Signal handler to call the cancel function on SIGINT and SIGTERM.