v0.3.0 - Sequence Alignment and Review Fixes

Summary

Feature and maintenance release adding a complete sequence alignment workflow powered by BWA and SAMtools, while also resolving review findings from v0.2.1 and improving overall CLI/TUI consistency.

Highlights

• Added a new alignment module with end-to-end workflow support: BWA index, BWA mem, BAM sorting, BAM indexing, and samtools flagstat.
• Added [Alignment] Sequence Alignment to the TUI main menu for interactive alignment execution.
• Added bioflow align for non-interactive CLI usage with --ref, --input, --output, and --threads options.
• Added structured alignment statistics output, including total reads, mapped reads, unmapped reads, and mapping rate.
• Added BWA index cache detection to skip redundant indexing when reference index files already exist.
• Added complete English and Chinese i18n coverage for the alignment workflow.
• Fixed CLI argument routing so invalid env subcommand combinations now return the correct argument error exit code.
• Fixed recursive batch formatting output collisions by generating unique output names for files from nested directories.
• Removed redundant preflight execution in TUI QC flow and simplified preflight control logic.
• Improved alignment pipeline safety by replacing shell-based piping with explicit subprocess pipelines for better path handling and error reporting.
• Removed release archives, checksum files, and test-only files from the repository branch to keep the published project tree minimal.
• Updated package version to 0.3.0.

Compatibility

• Python 3.9+
• Conda recommended for bio-tool management
• Alignment workflow requires bwa and samtools to be available in PATH
• Fully backward compatible with v0.2.1 for existing sequence formatting and QC workflows

Assets

• install.sh
• install.sh.sha256
• BioFlow-CLI-0.3.0.tar.gz
• BioFlow-CLI-0.3.0.tar.gz.sha256

Open Source

BioFlow-CLI is an open-source project released under the MIT License.