diff --git a/ChangeLog b/ChangeLog index f4bcf0b..4c7e049 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,11 +1,12 @@ Unreleased + * SemiBin: Support running SemiBin with strobealign-aemb + (--abundance/-a) * citation: Add citation subcommand * SemiBin1: Introduce separate SemiBin1 command * internal: Code simplification and refactor * deprecation: Deprecate --orf-finder=fraggenescan option * Update abundance normalization * SemiBin: do not use more processes than can be taken advantage of (#155) - * Support running SemiBin with strobealign-aemb Version 2.0.2 Oct 31 2023 by BigDataBiology * multi_easy_bin: Fix multi_easy_bin with --write-pre-recluster (#128) diff --git a/SemiBin/main.py b/SemiBin/main.py index fcbf55e..491846b 100644 --- a/SemiBin/main.py +++ b/SemiBin/main.py @@ -295,7 +295,7 @@ def parse_args(args, is_semibin2): dest='bams', default=None, ) - p.add_argument('-a', '--abundance', + p.add_argument('-a', '--abundance', '--abundances', required=False, nargs='*', help='Path to the abundance file from strobealign-aemb. This can only be used when samples used in binning above or equal 5.', diff --git a/docs/whatsnew.md b/docs/whatsnew.md index da53c56..a3b4912 100644 --- a/docs/whatsnew.md +++ b/docs/whatsnew.md @@ -1,5 +1,28 @@ # What's New +## Version 2.1.0 + +*Released Mar 6, 2024* + +Main new feature is adding support for using output of strobealign-aemb. + +Use of the `SemiBin` command (instead of `SemiBin2`) will continue to work, but +print a warning and set a delay to ask users to upgrade. + +### User-visible changes + +- Support running SemiBin with [strobealign-aemb](https://github.com/ksahlin/strobealign/releases/tag/v0.13.0) (`--abundance`/`-a`) +- Add `citation` subcommand +- Introduce separate `SemiBin1` command as use of `SemiBin` is now deprecated and will trigger a warning + +### Internal improvements +- Code simplification and refactor +- deprecation: Deprecate --orf-finder=fraggenescan option +- Update abundance normalization + +### Bugfixes +- SemiBin: do not use more processes than can be taken advantage of [#155](https://github.com/BigDataBiology/SemiBin/issues/155) + ## Version 2.0.2 *Released Oct 31, 2023*