[codex] Refresh docs for kfdevel merge - #166

Merged

kfuku52 merged 85 commits into

Jun 8, 2026

Commits on Mar 5, 2026

Split curate into wsfilter/csfilter/finalize with unified outlier plots

Kenji Fukushima
authored and
Kenji Fukushima
committed

Commits on Mar 7, 2026

Fix ETE taxonomy cache refresh

Kenji Fukushima
authored and
Kenji Fukushima
committed
Improve private FASTQ taxonomy inference

Kenji Fukushima
authored and
Kenji Fukushima
committed

Commits on Mar 8, 2026

Improve getfastq filtering workflow

Kenji Fukushima
authored and
Kenji Fukushima
committed
Bump version to 0.16.3

Kenji Fukushima
authored and
Kenji Fukushima
committed
Bump version to 0.16.4

Kenji Fukushima
authored and
Kenji Fukushima
committed
Remove R runtime and port pipeline to Python

Kenji Fukushima
authored and
Kenji Fukushima
committed
Implement latent_glm batch correction backend

Kenji Fukushima
authored and
Kenji Fukushima
committed
Bump version to 0.16.5

Kenji Fukushima
authored and
Kenji Fukushima
committed
Track wiki content in repository

Kenji Fukushima
authored and
Kenji Fukushima
committed

Commits on Mar 10, 2026

Commits on Mar 18, 2026

Commits on Mar 19, 2026

Improve zero-hit metadata diagnostics

Kenji Fukushima
authored and
Kenji Fukushima
committed
Reorganize config assets and yeast reports

Kenji Fukushima
authored and
Kenji Fukushima
committed
Fallback to public original FASTQ after fasterq failure

Kenji Fukushima
authored and
Kenji Fukushima
committed

Commits on Mar 21, 2026

Bump version to 0.16.12 and log fasterq-dump failures

Kenji Fukushima
authored and
Kenji Fukushima
committed
Require sra-tools 3 for getfastq

Kenji Fukushima
authored and
Kenji Fukushima
committed

Commits on Mar 22, 2026

Support oarfish long-read quant workflows

Kenji Fukushima
authored and
Kenji Fukushima
committed
Add shared download throttling and drop prefetch fallback

Kenji Fukushima
authored and
Kenji Fukushima
committed
Bump version to 0.16.14

Kenji Fukushima
authored and
Kenji Fukushima
committed
Prefer available getfastq download providers

Kenji Fukushima
authored and
Kenji Fukushima
committed

Commits on Mar 25, 2026

Commits on Mar 26, 2026

Add ENA/DDBJ SRA sources and spillover throttling
kfuku52
committed

Commits on Apr 1, 2026

Bump version to 0.16.20
kfuku52
committed

Commits on Apr 2, 2026

Fix upstream transcriptome regressions

kfuku52
and
Copilot
committed

Commits on Apr 10, 2026

Refine select queue tiers and exclude 3-prime RNA-seq
kfuku52
committed

Commits on Apr 15, 2026

Fix quant alias matching and empty fastq reuse

kfuku52
and
Copilot
committed

Commits on May 28, 2026

Commits on Jun 8, 2026