v0.13.0

0.13.0 (2023-04-17)

Features

• simpleaf workflow refresh + display version in simpleaf workflow list (c07bf99)

Bug Fixes

• change force update protocols estuary to an enum (b2a7e8f)
• improve workflow list and add --ext-codes flag to workflow run (a389e7f)

v0.12.0

0.12.0 (2023-04-10)

Features

• improve autodetection of index type (ed70433)
• improve logging when parsing commands from workflow description (083e714)
• improve logging when parsing commands from workflow description (0d91772)

v0.11.1

0.11.1 (2023-04-07)

Bug Fixes

• add submodule to cargo.toml (6475ced)

v0.11.0

0.11.0 (2023-04-07)

Features

• add --skip-steps, --start-at, --resume for simpleaf workflow, and add get-workflow-config program (be205b1)
• Add Active field to workflow (22e0096)
• add more arguments and improve external command execution (475aabf)
• allow streaming transformation of complex geometry (11e177b)
• bump seq_geom version and print xform stats (4055cb5)
• improve workflow doc (dd8f3c5)
• improve workflow logging (07f811a)
• simpleaf RunWorkflow (21dd9d8)

Bug Fixes

• add explicit_pl to allowed filter arguments (30f86e9)
• fix incorrect collate cmd log recorded in the simpleaf_quant_log.json (8f9a59f)
• toy reference dir in testing dataset (6a9ed0e)
• toy reference dir in testing dataset (095efcb)
• Update af_utils.rs (fff3b5e)
• update library call to get simplified description string (4d87286)

v0.10.0

0.10.0 (2023-02-12)

Features

• improve logging (5d20450)

Bug Fixes

• add --overwrite flag to index command (2340945)

v0.9.0

0.9.0 (2023-02-08)

Features

• attempt to infer t2g if not provided explicitly (656a84a)

Bug Fixes

• be more informative on command error (44fb9cb)
• fix duplicated short argument (64a3010)

v0.8.1

0.8.1 (2023-01-03)

Bug Fixes

• minor dep version bumps (e3d79fe)

v0.8.0

0.8.0 (2023-01-03)

Features

• switch to tracing for logging (01538c6)

Bug Fixes

• improve helping message (9a3d851)

v0.7.0

0.7.0 (2022-11-15)

Features

• quant from map and min-reads (0621a2d)

Notes

• The --refseq argument for the index command has been renamed to --ref-seq to have consistent hyphenation with other flags. The original --refseq flag was added as an alias for this argument, and so it should still work. However, the use of the non-hyphenated --refseq is deprecated and may be removed in the future.

v0.6.0

0.6.0 (2022-10-26)

Features

• create AF_HOME if needed in set-paths (0d5411b)
• create AF_HOME if needed in set-paths (742c2e2)
• create home dir if it doesn't exist (bae0d42)