Release Notes
Features
- Require alevin-fry 0.18.0 and expose its deterministic cell-barcode
correction policy, neighborhood, and confidence controls across ordinary
RNA, multiplex RNA, and ATAC processing.
- Expose independent sample-barcode correction controls for multiplex assays,
including Exact, Unique, and Frequency policies.
- Add stage-specific
--gpl-memory-limit, --gpl-tmp-dir, and
--collate-memory-limit resource overrides. Omitted values remain omitted
from child commands so alevin-fry owns protocol defaults.
- Validate confidence fractions/decimals and human-readable memory sizes before
mapping begins.
Compatibility and execution
- Keep the deprecated
--sample-correction-mode accepted but hidden. Its
exact and 1-edit values translate to the corresponding new alevin-fry
arguments; deprecated child spellings are never emitted.
- Use two threads as the practical minimum. Requests of zero or one warn, are
raised to two, and continue; a host report of one available thread also warns
and still attempts two.
- Resolve the effective thread count once per pipeline and pass it consistently
to mapping, permit-list generation, collation or ATAC sorting, and
quantification.
- Run MACS peak calling from
atac process only when --call-peaks is set;
ordinary ATAC processing no longer fails after producing its BED merely
because MACS is not installed.
- Retire the obsolete
release.sh; bump_and_publish.sh is now the sole
documented release entry point.
Documentation and testing
- Document barcode correction for standard RNA, multiplex/Flex, and ATAC, and
add strict rustdoc to CI.
- Add typed command-building helpers and coverage for omitted defaults,
explicit forwarding, legacy translation, stage-specific resources, and the
thread floor.
Install simpleaf 0.28.0
Install prebuilt binaries via shell script
curl --proto '=https' --tlsv1.2 -LsSf https://github.com/COMBINE-lab/simpleaf/releases/download/v0.28.0/simpleaf-installer.sh | sh
Download simpleaf 0.28.0
