Release notes v0.16.25

Release Notes for v0.16.25

These notes summarize the CLI line merged into master through PR #166.

Major Workflow Changes

• AMALGKIT is Python-only for the main pipeline. R scripts and R smoke tests have been removed.
• amalgkit config has been removed. Selection behavior now lives in one select_rules.tsv file.
• amalgkit curate has been replaced by the split workflow wsfilter -> csfilter -> finalize.
• amalgkit csca has been replaced by csfilter plus downstream finalize outputs.
• amalgkit rerun has been added to rerun failed targets recorded by sanity_report.json.

Workspace and Selection

• amalgkit dataset --name init creates a scaffold with species.tsv, organ_terms.tsv, select_rules.tsv, and standard workspace directories.
• amalgkit dataset --rule_set base|test|plantae|vertebrate exports bundled selection rules to out_dir/select_rules.tsv.
• amalgkit select reads select_rules.tsv through --select_rules_tsv and supports species-wise batch mode with summary, queue, and manifest outputs.

Metadata, FASTQ, and Quantification

• metadata supports one-off Entrez search strings and species-wise batch queries from --species_tsv.
• integrate scans local FASTQ directories and appends private runs to AMALGKIT metadata.
• getfastq supports NCBI, AWS, GCP, ENA, and DDBJ provider fallbacks.
• Shared download locks and provider concurrency caps help large multi-process runs.
• Optional MMseqs2 rRNA and contaminant filters can be ordered with --filter_order.
• quant auto-selects kallisto for short-read runs and oarfish for long-read runs when --quant_backend auto.
• Quant index builds use shared locks to avoid duplicate species/backend index builds under array jobs.

Filtering and Final Output

• merge consolidates run-level abundance files into per-species count, effective-length, and TPM tables.
• cstmm performs cross-species TMM normalization with BUSCO or orthogroup inputs.
• wsfilter performs within-species outlier filtering and writes filtered metadata plus QC PDFs.
• csfilter performs cross-species outlier filtering with BUSCO or orthogroup inputs.
• finalize exports final per-species expression tables and supports Python backends for no, sva, ruvseq, combatseq, and latent_glm; combatseq requires optional inmoose.

Validation and Recovery

• sanity checks getfastq, index, quant, merge, busco, and finalize outputs.
• rerun resolves missing or failed targets from sanity reports and writes rerun_manifest.json unless disabled with --manifest none.

Migration Summary

Old command	Current replacement
amalgkit config	amalgkit dataset --rule_set ... and select_rules.tsv
amalgkit curate	amalgkit wsfilter, amalgkit csfilter, amalgkit finalize
amalgkit csca	amalgkit csfilter and amalgkit finalize