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.
- 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
- Remove irods 4.2.10 from github actions test workflow
- Add JSON and HTML reports to archived files
- Add BAM indices (bai) to archived files
- Include archive creation script in automatic release
- Add default ignored directories 'Install_logs' and 'persistence'
- Remove run directories after a delay, if they are empty
- Automated GitHub release on tagging
- Add iRODS 4.2.11 to GitHub Actions workflow
- 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
- Support for adding iRODS metadata for PromethION-24 runs.
- Support for BAM files.
- support for BED files (compressed).
- iRODS 4.2.10 support.
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Build with Go.1.17
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Bump github.com/rs/zerolog from 1.21.0 to 1.26.1
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Bump github.com/onsi/ginkgo from 1.16.2 to 1.16.5
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Bump github.com/onsi/gomega from 1.11.0 to 1.17.0
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Bump github.com/spf13/cobra from 0.0.7 to 1.3.0
- Travis CI configuration.
- PromethION beta report parsing tests and unused test data.
- 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.
- RODS 4.1.12 support.
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Relocate repository from github.com/kjsanger to github.com/wtsi-npg
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Bump github.com/wtsi-npg/extendo/v2 from 2.2.0 to 2.4.0
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Bump github.com/wtsi-npg/logshim from to 1.1.0 to 1.3.0
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Bump github.com/wtsi-npg/logshim-zerolog from 1.1.0 to 1.3.0
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Bump github.com/klauspost/pgzip from 1.2.1 to 1.2.5
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Bump github.com/onsi/ginkgo from 1.12.3 to 1.16.1
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Bump github.com/onsi/gomega from 1.10.1 to 1.11.0
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Bump github.com/rs/zerolog from 1.19.1 to 1.21.0
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Bump github.com/spf13/cobra from 0.0.5 to 0.0.7
- PromethION support for enhanced metadata.
- iRODS 4.2.7 clients to the test matrix.
- "ont" namespace to iRODS metadata attributes.
- Bump github.com/wtsi-npg/extendo from 2.1.0 to 2.2.0
- experiment_name and instrument_slot to report metadata.
- 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
- A systemd unit template and wrapper script.
- A String method to WorkPlan.
- Logging immediately before and after a work function is called.
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Improve verbose level logging for consistency and information.
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Add to default paths to ignore in the data root.
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Bump github.com/wtsi-npg/extendo from 1.1.0 to 2.0.0
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Bump github.com/onsi/ginkgo from 1.10.3 to 1.12.0
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Bump github.com/onsi/gomega from 1.7.1 to 1.9.0
- 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.
- 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.
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Use pgzip implementation.
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Bump github.com/wtsi-npg/extendo from 1.0.0 to 1.1.0
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Bump github.com/onsi/gomega from 1.5.0 to 1.7.1
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Bump github.com/onsi/ginkgo from 1.8.0 to 1.10.3
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Bump github.com/rs/zerolog from 1.14.3 to 1.17.2
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Bump github.com/stretchr/testify from 1.3.0 to 1.4.0
- 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.
- 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.