v0.2.1

0.2.1 (2024-11-12)

Bug Fixes

• add tidyr, update and pin (a6ac043)

Performance Improvements

• group fastp and star align. modify profile so it only handles integers (5e0e6f9)
• run reads in the head node (4dc4b18)

v0.2.0

0.2.0 (2024-08-06)

Features

• pin dependencies (123de53)

v0.1.0

0.1.0 (2024-05-22)

Features

• cache references and index; extract to profile (74d1352)
• disable default adapters (e1f347c)
• environments: update everything (9c05755)
• fastp: compress with pigz (8d78a69)
• fastp: if adaptors are empty, assume the default ones (ec0a097)
• folders: reorganize properly (2528242)
• gha: name cache (09ba04e)
• gha: sort lines (edcd963)
• gha: split into steps (faa3a4b)
• modify yaml to be with : notation (b031d87)
• move profile to new location (ee1a01e)
• preprocess: add pigz (4de4181)
• preprocess: rename rules; extract resources to profile (7d39061)
• preprocess: update env (2fc671f)
• quantify: no more folder per library (f50e4f0)
• quantify: remove protected files (256db4c)
• quantify: rename rules; extract resources to profile; separate index and align (4c28057)
• raise latency to 1 min (c9fe9c4)
• readme: precommit everything (c3820a3)
• readme: update everything (ec9d548)
• reduce samples to speed up testing (230dae9)
• reference: rename rules, readability (f279335)
• renaming: wrong rule names (eb9853c)
• restructure repo (48819d8)
• rulegraph: update (c4aa33e)
• run: add local run script (be1bf21)
• sample_id, library_id (8a898f3)
• sample: simplify test dataset (a3a1308)
• update and lint environments (227929c)
• update rules to new nomenclature (35a5445)
• update rules to new nomenclature (af5e988)

Bug Fixes

• gha: back to custom action (0f5c371)
• gha: check GHA now that snakemake 8.1.0 is published (6f2b880)
• gha: disable cache removal; upgrade pre-commit (12d114c)
• gha: point action to just v1 (4d82cfe)
• gha: put the downloading into a signle line (dcbdd42)
• gha: put the downloading into a signle line (cf846b5)
• gha: reorder lines again (45043bf)
• gha: typo (339cb5c)
• gha: update caching action to the custom repo (559109a)
• gha: update snakemake action to 1.25.1 (2903a78)
• gha: use temporary action (acb06c6)
• linting (f137425)
• remove output dir (e889ed9)
• rename rules (0b223af)
• report: downgrade python (b61b282)
• report: use correct report names (04364fb)

v0.0.1

Initial release for 3D'omics