v5.1.0

What's Changed

• Upgrade to latest static analysis Action by @nwiltsie in #96
• Add diagram by @yashpatel6 in #83
• add support for unmmapped bams by @zhuchcn in #98
• Compression MIME addition and checksum identification expanded by @yashpatel6 in #99

New Contributors

• @zhuchcn made their first contribution in #98

Full Changelog: v5.0.0...v5.1.0

v5.0.0

What's Changed

• Checksum flag by @yashpatel6 in #95

Full Changelog: v5.0.0-rc.3...v5.0.0

v5.0.0-rc.3

What's Changed

• Compression integrity checks by @yashpatel6 in #93

Full Changelog: v5.0.0-rc.2...v5.0.0-rc.3

v5.0.0-rc.2

What's Changed

• FASTQ Validator by @yashpatel6 in #89

Full Changelog: v5.0.0-rc.1...v5.0.0-rc.2

v5.0.0-rc.1

What's Changed

• Refactor interface by @yashpatel6 in #88

Full Changelog: v4.0.0...v5.0.0-rc.1

v4.0.0

What's Changed

• Autofix broken Confluence links by @nwiltsie in #84
• Update CICD-base.yaml by @nwiltsie in #85
• Parallelize validation by @yashpatel6 in #86

New Contributors

• @nwiltsie made their first contribution in #84

Full Changelog: v4.0.0-rc.2...v4.0.0

v4.0.0-rc.2

What's Changed

Changed

• Resolve potential symlinks before validation

Full Changelog: v4.0.0-rc.1...v4.0.0-rc.2

v4.0.0-rc.1

What's Changed

Added

• Add check for empty BAM files (valid header but no reads).
• Add auto-build workflow to push image to uclahs-cds registry
• Add repo source label to Dockerfile
• Add check for existence of index file
• Add references for VCFtools and Pysam in README
• Unit tests for existing functions
• Unit tests for main runner functions
• Add separate checks for SAM and CRAM files
• Compression validation and detection through python-magic

Changed

• Make -t optional, default to file-input
• Explicitly set Python version to 3.10
• Split validation and checksum generation into different CLI commands
• Re-organize functions
• Change builder image to mambaforge in Dockerfile
• Update README input tables and command examples
• Re-structure README with details of current tool

Fixed

Removed

• Remove deprecated parameter options from README
• Remove inaccessible design doc link from README
• Remove directory checking
• Remove user-specified file type option

Full Changelog: v3.0.0...v4.0.0-rc.1

v3.0.0

What's Changed

Updated

• Updated bl-base to 1.1.0
• Installed tools using mamba

Added

• Add bldocker user and group to Dockerfile
• Add support for mutliple input files

Changed

• Convert module to Python CLI package; now runs directly from commandline with validate.
• Single source package version from __init__.py
• Use pysam instead of samtools in bam file validation.

Fixed

• Add handling for valid file types whose validation is not yet implemented.

New Contributors

• @aybeshlikyan made their first contribution in #29

Full Changelog: v2.1.6...v3.0.0

v2.1.6 [recommended]

File type detection update to properly detect file type when filename contains multiple .
Fixed bug with detecting fasta files

Docker image: blcdsdockerregistry/pipeval:2.1.6