v2.0.0-beta27 Release

2.0.0-beta27 - 2026-03-18

f03804b...7d9a12d

Features

• Add a test version of dbcan3 to compare against dbcan2 (efb3cc2)

  dbcan3 and dbcan3-sub test versions, will run both if run_dbcan3
  option is present.

• Switch hmmsearch to using PyHMMER search (7d9a12d)

  PyHMMER has better parrallelism support, directly calling
  the lower level C bindings for HMMER and rewriting how
  it parallelizes. This means that when you had cpus=4 arg, it can
  1/3 of the walltime with the exact same result.

v2.0.0-beta26 Release

2.0.0-beta26 - 2026-03-09

605d4f5...91edea7

Features

• Add ag heatmap output (91edea7)

  Update dram_viz version to support new ag viz rules format.
  When users run ag summarize, output ag visualization.
  Add parameters to pass in custom rules sheets.

Package

• Add pre-commit for lint/formatting and lint/format package (c7c030a)

v2.0.0-beta25 Release

2.0.0-beta25 - 2026-03-04

Highlights

Bugfixes for utilizing --input_genes instead of --input_fasta. Various subtle
problems and edge cases with using --input_genes, also now new ability to use
--rename on already called genes with --input_genes.

c95aa83...d8d3cb8

Bug Fixes

• Bugfixes for using input_genes parameter (d8d3cb8)

• Skip tRNA and rRNA when using input_genes unless trna and rrna
  input sheet provided since they require raw fasta file to produce.

• new parse_faa file to generate called_table summary file
  that leave error message on non-zero exit code telling people
  to check the headers metadata in case they don't match with prodigal
  output metadata.

• use the same parsing code parse_faa.sh from above to generate
  sumamry table for DRAM if using input_fasta and input_genes so
  less likely of bug in one spot isn't noticed if other is working.

• fix bugs where downstream stuff would pass dummy sheet to summarize
  and then that wouldn't properly handle it

• add ability to rename headers with input_genes with --rename flag
  with rename_headers.py script and rename_proteins.nf

v2.0.0-beta24 Release

2.0.0-beta24 - 2026-02-03

3659fda...32d0527

Bug Fixes

• Bugfix for excel saving when rrna or trna are None (32d0527)

V2.0.0-beta23 Release

2.0.0-beta23 - 2026-02-01

348e276...852e0ae

Features

• Add new DRAM rule parser submodule for traits and distill (5e9a088)

New python Lark base rule parser that defines rule grammer
for traits grammer that can be reused for distill and product.
This rule parser is more accurate and less error prone than
the older traits parser completely custom coded. THis fixes
a number of bugs where things were being double counted and not
parsed correctly. This also allows distill, traits, and product
eventually to all use the same rule parsing code. Rule parsing
documentation can be found in docs/rules_parser.md or
https://dramit.readthedocs.io/en/latest/rules_parser.html

Rule parser is implemented with polars instead of Pandas for a
few reasons. It is a bit faster, and it allows lazy query planning.
The annotation df is not currently lazy (eager rn), but with plans
to allow it to be lazy. Lazy DataFrames can be more memory efficient
by only loading the data/columns needed, and doing query optimization
to speed up and require less memory for intermediate steps.

• Update summarize eco Ag sheet to newly developed Ag sheet (4937f1c)

• Add carbon rules to traits, save traits as excel sheet (02de665)

Package

• Package cleanup. Removing old files and cleanups (c6bae64)

v2.0.0-beta22 Release

What's Changed

• Bugfix/info sheet a rank fix by @madeline-scyphers in #479

Full Changelog: v2.0.0-beta21...v2.0.0-beta22

v2.0.0-beta21

What's Changed

• Update sphinx theme by @madeline-scyphers in #470
• fix: rrna scan e_value and strand column order fix by @madeline-scyphers in #471
• test: add integration test for summarize by @madeline-scyphers in #475
• fix: traits and vis can now be ran with w/o summarize by @madeline-scyphers in #476
• fix: hmm top hit fix and metals hmm db by @madeline-scyphers in #478

Full Changelog: v2.0.0-beta19...v2.0.0-beta21

v2.0.0-beta19 Release

What's Changed

• Package/rename pipeline steps by @madeline-scyphers in #463
• package(api): add full_mode to profiles to run all options by @madeline-scyphers in #464
• fix: Add back in genome_stats, fix trna counts by @madeline-scyphers in #466
• fix: small bgfixes for namespace errors, error messages, and cli by @madeline-scyphers in #467
• package: Update MMSEQS2 and API documentation by @madeline-scyphers in #468
• bugfix: Fix distill bugs with genome stats, and metabolism summary by @madeline-scyphers in #469

Full Changelog: v2.0.0-beta17...v2.0.0-beta19

v2.0.0-beta17 Release

What's Changed

• fix: Allow calling quast with arbitrary large no of inputs by @madeline-scyphers in #456
• feat: Rename ID col in GFF file by @madeline-scyphers in #457

Full Changelog: v2.0.0-beta16...v2.0.0-beta17

v2.0.0-beta16 Release

What's Changed

• Add changelog to repo and docs by @madeline-scyphers in #443
• feat(testing): Add nf-test by @madeline-scyphers in #444
• bug: Fix TRNA_COLLECT and COMBINE_ANNOTATIONS for large # inputs by @madeline-scyphers in #447

Full Changelog: v2.0.0-beta15...v2.0.0-beta16
https://github.com/WrightonLabCSU/DRAM/blob/dev/CHANGELOG.md