diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
deleted file mode 100644
index e352fab..0000000
--- a/.github/ISSUE_TEMPLATE/bug_report.md
+++ /dev/null
@@ -1,19 +0,0 @@
----
-name: Bug report
-about: Report an issue with this extension
-title: ''
-labels: bug
-
----
-
-**Describe the bug**
-A clear and concise description of what the bug is.
-
-**Output/logs/screenshots**
-Please include any relevant output.
-
-**Sunbeam version**
-Get version by activating sunbeam environment and running `sunbeam --version`.
-
-**Additional context**
-Add any other context about the problem here.
diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md
deleted file mode 100644
index bba4070..0000000
--- a/.github/ISSUE_TEMPLATE/feature_request.md
+++ /dev/null
@@ -1,12 +0,0 @@
----
-name: Feature request
-about: Suggest an idea for this extension
-title: ''
-labels: enhancement
-
----
-
-**What's the feature?**
-
-**Additional context**
-Add any other context or screenshots about the feature request here.
diff --git a/.github/ISSUE_TEMPLATE/other.md b/.github/ISSUE_TEMPLATE/other.md
deleted file mode 100644
index fee03e7..0000000
--- a/.github/ISSUE_TEMPLATE/other.md
+++ /dev/null
@@ -1,9 +0,0 @@
----
-name: Other
-about: Not a bug report or feature request
-title: ''
-labels: ''
-
----
-
-
diff --git a/.github/workflows/condabot.yml b/.github/workflows/condabot.yml
new file mode 100644
index 0000000..bf044aa
--- /dev/null
+++ b/.github/workflows/condabot.yml
@@ -0,0 +1,16 @@
+name: Condabot
+
+on:
+  schedule:
+    - cron: '0 2 * * 1'
+  workflow_dispatch:
+
+jobs:
+  run-condabot:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+            fetch-depth: 0
+      - uses: sunbeam-labs/condabot@v1
\ No newline at end of file
diff --git a/.github/workflows/pr.yml b/.github/workflows/pr.yml
deleted file mode 100644
index d9dd671..0000000
--- a/.github/workflows/pr.yml
+++ /dev/null
@@ -1,14 +0,0 @@
-name: Tests
-
-on:
-    pull_request:
-      branches:
-        - main
-    push:
-      branches:
-        - main
-
-jobs:
-    run-tests:
-        uses: ./.github/workflows/tests.yml
-        secrets: inherit
\ No newline at end of file
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 2975c61..dd7b5e5 100755
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -1,74 +1,31 @@
 name: Tests
 
 on:
+  workflow_dispatch:
+
   pull_request:
-    branches: [ master, main ]
+    branches: [ main, master ]
   push:
-    branches: [ master, main ]
-  workflow_call:
-  workflow_dispatch:
-  schedule:
-    - cron: "0 13 * * 1"
+    branches: [ main, master ]
 
 jobs:
-  lint:
-    name: Lint Code
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Checkout Code
-        uses: actions/checkout@v4
-      
-      - uses: actions/setup-python@v5
-        with:
-            python-version: 3.12
-
-      - name: Install Dependencies
-        run: pip install black snakefmt
-
-      - name: Run Linter
-        run: |
-          black --check .
-          snakefmt --check *.smk
-
-  test-unit:
-    name: Run Extension Unit Tests
+  test:
+    name: Test
     runs-on: ubuntu-latest
 
     steps:
       - name: Checkout Code
         uses: actions/checkout@v4
       
-      - uses: actions/setup-python@v5
-        with:
-            python-version: 3.12
-      
-      - name: Install Dependencies
-        run: pip install pytest pandas
-
-      - name: Run Unit Tests
-        run: pytest .tests/unit/
-
-  test-e2e:
-    name: Test Extension with Sunbeam
-    runs-on: ubuntu-latest
-    needs:
-      - test-unit
-      - lint
-
-    steps:
-      - name: Checkout Code
-        uses: actions/checkout@v4
-        
-      - name: Test with Sunbeam
+      - name: Sunbeam tests
         uses: sunbeam-labs/sbx_test_action@v1
 
       - name: Dump Logs
         shell: bash
         if: always()
-        run: tail -n +1 logs/*
+        run: tail -n +1 logs/* || true
       
       - name: Dump Stats
         shell: bash
         if: always()
-        run: cat stats/*
\ No newline at end of file
+        run: cat stats/* || true
diff --git a/.tests/e2e/test_dry_run.py b/.tests/e2e/test_dry_run.py
index 95d2798..a170524 100755
--- a/.tests/e2e/test_dry_run.py
+++ b/.tests/e2e/test_dry_run.py
@@ -1,3 +1,4 @@
+import os
 import pytest
 import shutil
 import subprocess as sp
@@ -6,14 +7,8 @@
 
 
 @pytest.fixture
-def setup(monkeypatch):
+def setup():
     temp_dir = Path(tempfile.mkdtemp())
-    monkeypatch.setenv(
-        "SUNBEAM_EXTENSIONS", str(Path(__file__).parent.parent.parent.parent.resolve())
-    )
-    print(
-        "SUNBEAM_EXTENSIONS:", str(Path(__file__).parent.parent.parent.parent.resolve())
-    )
 
     reads_fp = Path(".tests/data/reads/").resolve()
 
@@ -22,8 +17,6 @@ def setup(monkeypatch):
     sp.check_output(["sunbeam", "init", "--data_fp", reads_fp, project_dir])
 
     config_fp = project_dir / "sunbeam_config.yml"
-    with open(config_fp, "r") as f:
-        print("Initial config file content:", f.read())
 
     config_str = f"sbx_sga: {{mash_ref: '{temp_dir}/dummy.msh'}}"
     Path(temp_dir / "dummy.msh").touch()
@@ -94,15 +87,12 @@ def run_sunbeam(setup):
     print("STDOUT: ", sbx_proc.stdout)
     print("STDERR: ", sbx_proc.stderr)
 
-    try:
-        shutil.copytree(log_fp, "logs/")
-        shutil.copytree(stats_fp, "stats/")
-    except FileNotFoundError:
-        print("No logs or stats directory found.")
-        Path("logs/").mkdir(parents=True, exist_ok=True)
-        Path("stats/").mkdir(parents=True, exist_ok=True)
-        Path("logs/file").touch()
-        Path("stats/file").touch()
+    if os.getenv("GITHUB_ACTIONS") == "true":
+        try:
+            shutil.copytree(log_fp, "logs/")
+            shutil.copytree(stats_fp, "stats/")
+        except FileNotFoundError:
+            print("No logs or stats directory found.")
 
     output_fp = project_dir / "sunbeam_output"
     benchmarks_fp = project_dir / "stats/"
diff --git a/README.md b/README.md
index 0617218..488ff61 100644
--- a/README.md
+++ b/README.md
@@ -4,6 +4,7 @@
 
 <!-- Badges start -->
 [![Tests](https://github.com/sunbeam-labs/sbx_sga/actions/workflows/tests.yml/badge.svg)](https://github.com/sunbeam-labs/sbx_sga/actions/workflows/tests.yml)
+![Condabot](https://img.shields.io/badge/condabot-active-purple)
 [![DockerHub](https://img.shields.io/docker/pulls/sunbeamlabs/sbx_sga)](https://hub.docker.com/repository/docker/sunbeamlabs/sbx_sga/)
 <!-- Badges end -->
 
@@ -11,37 +12,12 @@
 
 sbx_sga (Single Genome Assembly) is a [sunbeam](https://github.com/sunbeam-labs/sunbeam) extension for isolate QC, assembly, and classification. This pipeline uses [Mash](https://github.com/marbl/mash) for quality control, [Shovill](https://github.com/tseemann/shovill) for bacterial isolate assembly, [CheckM2](https://github.com/chklovski/CheckM2) and [QUAST](https://github.com/ablab/quast) for assembly QC, [MLST](https://github.com/tseemann/mlst) for typing, [Bakta](https://github.com/oschwengers/bakta) for annotation, [abriTAMR](https://github.com/MDU-PHL/abritamr) for AMR profiling, and [Sylph](https://github.com/bluenote-1577/sylph) for taxonomic classification.
 
-## Installation
-
-Extension install is as simple as passing the extension's URL on GitHub to `sunbeam extend`:
-
-    sunbeam extend https://github.com/sunbeam-labs/sbx_sga
-
-Any user-modifiable parameters specified in `config.yml` are automatically added on `sunbeam init`. If you're installing an extension in a project where you already have a config file, run the following to add the options for your newly added extension to your config (the `-i` flag means in-place config file modification; remove the `-i` flag to see the new config in stdout):
-
-    sunbeam config update -i /path/to/project/sunbeam_config.yml
-
-Installation instructions for older versions of Sunbeam are included at the end of this README.
-
-## Running
-
-To run an extension, simply run Sunbeam as usual with your extension's target rule specified:
-
-    sunbeam run --profile /path/to/project/ example_rule
-
-### Options for config.yml
+## Config
 
   - mash_ref: the reference file for running Mash (should be a file ending in `.msh`)
   - checkm_ref: the diamond database for running CheckM2 (should be a file ending in `.dmnd`)
   - bakta_ref: the bakta reference database (should be a directory similar to `.../bakta_db/db/`)
     
-## Installing an extension (legacy instructions for sunbeam <3.0)
-
-Installing an extension is as simple as cloning (or moving) your extension directory into the sunbeam/extensions/ folder, installing requirements through Conda, and adding the new options to your existing configuration file: 
-
-    git clone https://github.com/sunbeam-labs/sbx_sga/ sunbeam/extensions/sbx_sga
-    cat sunbeam/extensions/sbx_sga/config.yml >> sunbeam_config.yml
-
-## Issues with pipeline
+## Docs
 
-Please post any issues with this extension [here](https://github.com/sunbeam-labs/sbx_sga/issues).
+More [docs](https://sunbeam.readthedocs.io/en/stable/extensions.html).
\ No newline at end of file
diff --git a/envs/abritamr.yml b/envs/abritamr.yml
index 59fbe47..5d11f44 100644
--- a/envs/abritamr.yml
+++ b/envs/abritamr.yml
@@ -2,91 +2,5 @@ name: sga_abritamr
 channels:
   - conda-forge
   - bioconda
-  - defaults
-  - r
 dependencies:
-  - _libgcc_mutex=0.1
-  - _openmp_mutex=4.5
-  - abritamr=1.0.11
-  - blast=2.15.0
-  - bzip2=1.0.8
-  - c-ares=1.28.1
-  - ca-certificates=2024.2.2
-  - curl=7.88.1
-  - entrez-direct=21.6
-  - gettext=0.22.5
-  - gettext-tools=0.22.5
-  - hmmer=3.4
-  - keyutils=1.6.1
-  - krb5=1.20.1
-  - ld_impl_linux-64=2.40
-  - libasprintf=0.22.5
-  - libasprintf-devel=0.22.5
-  - libblas=3.9.0
-  - libcblas=3.9.0
-  - libcurl=7.88.1
-  - libedit=3.1.20191231
-  - libev=4.33
-  - libffi=3.4.2
-  - libgcc-ng=13.2.0
-  - libgettextpo=0.22.5
-  - libgettextpo-devel=0.22.5
-  - libgfortran-ng=13.2.0
-  - libgfortran5=13.2.0
-  - libgomp=13.2.0
-  - libidn2=2.3.7
-  - liblapack=3.9.0
-  - libnghttp2=1.58.0
-  - libnsl=2.0.1
-  - libopenblas=0.3.27
-  - libsqlite=3.45.3
-  - libssh2=1.11.0
-  - libstdcxx-ng=13.2.0
-  - libunistring=0.9.10
-  - libxcrypt=4.4.36
-  - libzlib=1.2.13
-  - ncbi-amrfinderplus=3.10.16
-  - ncbi-vdb=3.1.1
-  - ncurses=6.5
-  - numpy=1.21.6
-  - openssl=3.3.0
-  - pandas=1.3.5
-  - pcre=8.45
-  - perl=5.32.1
-  - perl-archive-tar=2.40
-  - perl-carp=1.50
-  - perl-common-sense=3.75
-  - perl-compress-raw-bzip2=2.201
-  - perl-compress-raw-zlib=2.202
-  - perl-encode=3.21
-  - perl-exporter=5.74
-  - perl-exporter-tiny=1.002002
-  - perl-extutils-makemaker=7.70
-  - perl-io-compress=2.201
-  - perl-io-zlib=1.14
-  - perl-json=4.10
-  - perl-json-xs=2.34
-  - perl-list-moreutils=0.430
-  - perl-list-moreutils-xs=0.430
-  - perl-parent=0.241
-  - perl-pathtools=3.75
-  - perl-scalar-list-utils=1.63
-  - perl-storable=3.15
-  - perl-types-serialiser=1.01
-  - pip=24.0
-  - python=3.7.12
-  - python-dateutil=2.9.0
-  - python_abi=3.7
-  - pytz=2024.1
-  - readline=8.2
-  - setuptools=59.8.0
-  - six=1.16.0
-  - sqlite=3.45.3
-  - tk=8.6.13
-  - wget=1.21.4
-  - wheel=0.34.2
-  - xlsxwriter=3.1.9
-  - xz=5.2.6
-  - zlib=1.2.13
-  - zstd=1.5.6
-
+  - abritamr
\ No newline at end of file
diff --git a/envs/bakta.yml b/envs/bakta.yml
index fd530a4..4028f93 100644
--- a/envs/bakta.yml
+++ b/envs/bakta.yml
@@ -2,161 +2,5 @@ name: sga_bakta
 channels:
   - conda-forge
   - bioconda
-  - defaults
-  - r
 dependencies:
-  - _libgcc_mutex=0.1
-  - _openmp_mutex=4.5
-  - alive-progress=1.6.2
-  - aragorn=1.2.41
-  - bakta=1.7.0
-  - biopython=1.83
-  - blast=2.15.0
-  - brotli-python=1.1.0
-  - bzip2=1.0.8
-  - c-ares=1.28.1
-  - ca-certificates=2024.6.2
-  - certifi=2024.2.2
-  - charset-normalizer=3.3.2
-  - circos=0.69.9
-  - curl=8.8.0
-  - diamond=2.1.8
-  - entrez-direct=21.6
-  - expat=2.6.2
-  - font-ttf-dejavu-sans-mono=2.37
-  - font-ttf-inconsolata=3.000
-  - font-ttf-source-code-pro=2.038
-  - font-ttf-ubuntu=0.83
-  - fontconfig=2.14.2
-  - fonts-conda-ecosystem=1
-  - fonts-conda-forge=1
-  - freetype=2.12.1
-  - gettext=0.22.5
-  - gettext-tools=0.22.5
-  - giflib=5.2.2
-  - hmmer=3.4
-  - icu=73.2
-  - idna=3.7
-  - infernal=1.1.5
-  - isa-l=2.31.0
-  - keyutils=1.6.1
-  - krb5=1.21.2
-  - ld_impl_linux-64=2.40
-  - lerc=4.0.0
-  - libasprintf=0.22.5
-  - libasprintf-devel=0.22.5
-  - libblas=3.9.0
-  - libcblas=3.9.0
-  - libcurl=8.8.0
-  - libdeflate=1.20
-  - libedit=3.1.20191231
-  - libev=4.33
-  - libexpat=2.6.2
-  - libffi=3.4.2
-  - libgcc-ng=13.2.0
-  - libgd=2.3.3
-  - libgettextpo=0.22.5
-  - libgettextpo-devel=0.22.5
-  - libgfortran-ng=13.2.0
-  - libgfortran5=13.2.0
-  - libgomp=13.2.0
-  - libidn2=2.3.7
-  - libjpeg-turbo=3.0.0
-  - liblapack=3.9.0
-  - libnghttp2=1.58.0
-  - libnsl=2.0.1
-  - libopenblas=0.3.27
-  - libpng=1.6.43
-  - libsqlite=3.45.3
-  - libssh2=1.11.0
-  - libstdcxx-ng=13.2.0
-  - libtiff=4.6.0
-  - libunistring=0.9.10
-  - libuuid=2.38.1
-  - libwebp=1.4.0
-  - libwebp-base=1.4.0
-  - libxcrypt=4.4.36
-  - libzlib=1.2.13
-  - ncbi-amrfinderplus=3.11.26
-  - ncbi-vdb=3.1.1
-  - ncurses=6.5
-  - numpy=1.26.4
-  - openssl=3.3.1
-  - pbzip2=1.1.13
-  - pcre=8.45
-  - perl=5.32.1
-  - perl-archive-tar=2.40
-  - perl-b-cow=0.007
-  - perl-carp=1.50
-  - perl-clone=0.46
-  - perl-common-sense=3.75
-  - perl-compress-raw-bzip2=2.201
-  - perl-compress-raw-zlib=2.202
-  - perl-config-general=2.65
-  - perl-digest-perl-md5=1.9
-  - perl-encode=3.21
-  - perl-exporter=5.74
-  - perl-exporter-tiny=1.002002
-  - perl-extutils-config=0.008
-  - perl-extutils-helpers=0.026
-  - perl-extutils-installpaths=0.012
-  - perl-extutils-makemaker=7.70
-  - perl-extutils-pl2bat=0.005
-  - perl-font-ttf=1.06
-  - perl-gd=2.76
-  - perl-inc-latest=0.500
-  - perl-io-compress=2.201
-  - perl-io-string=1.08
-  - perl-io-zlib=1.14
-  - perl-json=4.10
-  - perl-json-xs=2.34
-  - perl-list-moreutils=0.430
-  - perl-list-moreutils-xs=0.430
-  - perl-math-bezier=0.01
-  - perl-math-round=0.07
-  - perl-math-vecstat=0.08
-  - perl-module-build=0.4232
-  - perl-module-build-tiny=0.039
-  - perl-module-implementation=0.09
-  - perl-module-runtime=0.016
-  - perl-number-format=1.76
-  - perl-params-validate=1.31
-  - perl-parent=0.241
-  - perl-pathtools=3.75
-  - perl-readonly=2.05
-  - perl-regexp-common=2017060201
-  - perl-scalar-list-utils=1.63
-  - perl-set-intspan=1.19
-  - perl-statistics-basic=1.6611
-  - perl-storable=3.15
-  - perl-svg=2.87
-  - perl-test-fatal=0.016
-  - perl-text-format=0.62
-  - perl-time-hires=1.9764
-  - perl-try-tiny=0.31
-  - perl-types-serialiser=1.01
-  - perl-xml-parser=2.44_01
-  - pigz=2.8
-  - piler-cr=1.06
-  - pip=24.0
-  - pyrodigal=2.1.0
-  - pysocks=1.7.1
-  - python=3.10.14
-  - python-isal=1.6.1
-  - python_abi=3.10
-  - pyyaml=6.0.1
-  - readline=8.2
-  - requests=2.32.3
-  - setuptools=70.0.0
-  - tk=8.6.13
-  - trnascan-se=2.0.11
-  - tzdata=2024a
-  - urllib3=2.2.1
-  - wget=1.21.4
-  - wheel=0.43.0
-  - xopen=1.6.0
-  - xz=5.2.6
-  - yaml=0.2.5
-  - zlib=1.2.13
-  - zstd=1.5.6
-
+  - bakta
\ No newline at end of file
diff --git a/envs/checkm2.yml b/envs/checkm2.yml
index e33b508..47b66a3 100644
--- a/envs/checkm2.yml
+++ b/envs/checkm2.yml
@@ -2,126 +2,5 @@ name: sga_checkm2
 channels:
   - conda-forge
   - bioconda
-  - defaults
-  - r
 dependencies:
-  - _libgcc_mutex=0.1
-  - _openmp_mutex=4.5
-  - abseil-cpp=20200923.3
-  - aiohttp=3.9.5
-  - aiosignal=1.3.1
-  - astor=0.8.1
-  - astunparse=1.6.3
-  - async-timeout=4.0.3
-  - attrs=23.2.0
-  - blinker=1.8.2
-  - boost-cpp=1.70.0
-  - brotli-python=1.1.0
-  - bzip2=1.0.8
-  - c-ares=1.28.1
-  - ca-certificates=2024.6.2
-  - cachetools=4.2.4
-  - certifi=2024.2.2
-  - cffi=1.16.0
-  - charset-normalizer=3.3.2
-  - click=8.1.7
-  - colorama=0.4.6
-  - cryptography=39.0.0
-  - diamond=2.0.4
-  - frozenlist=1.4.1
-  - gast=0.3.3
-  - giflib=5.2.2
-  - google-auth=1.35.0
-  - google-auth-oauthlib=0.4.6
-  - google-pasta=0.2.0
-  - grpc-cpp=1.36.4
-  - grpcio=1.36.1
-  - h5py=2.10.0
-  - hdf5=1.10.6
-  - icu=64.2
-  - idna=3.7
-  - importlib-metadata=7.1.0
-  - joblib=1.4.2
-  - jpeg=9e
-  - keras-preprocessing=1.1.2
-  - keyutils=1.6.1
-  - krb5=1.20.1
-  - ld_impl_linux-64=2.40
-  - libblas=3.9.0
-  - libcblas=3.9.0
-  - libcurl=7.87.0
-  - libedit=3.1.20191231
-  - libev=4.33
-  - libffi=3.4.2
-  - libgcc-ng=13.2.0
-  - libgfortran-ng=13.2.0
-  - libgfortran5=13.2.0
-  - libgomp=13.2.0
-  - liblapack=3.9.0
-  - libnghttp2=1.51.0
-  - libnsl=2.0.1
-  - libopenblas=0.3.25
-  - libpng=1.6.43
-  - libprotobuf=3.15.8
-  - libsqlite=3.45.3
-  - libssh2=1.10.0
-  - libstdcxx-ng=13.2.0
-  - libuuid=2.38.1
-  - libzlib=1.2.13
-  - lightgbm=3.2.1
-  - markdown=3.6
-  - markupsafe=2.1.5
-  - multidict=6.0.5
-  - ncurses=6.5
-  - oauthlib=3.2.2
-  - openssl=1.1.1w
-  - opt_einsum=3.3.0
-  - packaging=24.0
-  - pandas=1.4.0
-  - pip=24.0
-  - prodigal=2.6.3
-  - protobuf=3.15.8
-  - pyasn1=0.6.0
-  - pyasn1-modules=0.4.0
-  - pycparser=2.22
-  - pyjwt=2.8.0
-  - pyopenssl=23.2.0
-  - pysocks=1.7.1
-  - python=3.8.15
-  - python-dateutil=2.9.0
-  - python-flatbuffers=1.12
-  - python_abi=3.8
-  - pytz=2024.1
-  - pyu2f=0.1.5
-  - re2=2021.04.01
-  - readline=8.2
-  - requests=2.32.3
-  - requests-oauthlib=2.0.0
-  - rsa=4.9
-  - scikit-learn=0.23.2
-  - scipy=1.8.0
-  - setuptools=70.0.0
-  - snappy=1.1.10
-  - tensorboard=2.4.1
-  - tensorboard-plugin-wit=1.8.1
-  - tensorflow=2.4.0
-  - tensorflow-base=2.4.0
-  - tensorflow-estimator=2.4.0
-  - threadpoolctl=3.5.0
-  - tk=8.6.13
-  - tqdm=4.66.4
-  - urllib3=2.2.1
-  - werkzeug=3.0.3
-  - wheel=0.43.0
-  - xz=5.2.6
-  - yarl=1.9.4
-  - zipp=3.17.0
-  - zlib=1.2.13
-  - pip:
-      - absl-py==0.15.0
-      - checkm2==1.0.1
-      - numpy==1.23.5
-      - six==1.15.0
-      - termcolor==1.1.0
-      - typing-extensions==3.7.4.3
-      - wrapt==1.12.1
+  - checkm2
\ No newline at end of file
diff --git a/sbx_sga.smk b/sbx_sga.smk
index 1188ad4..b021699 100644
--- a/sbx_sga.smk
+++ b/sbx_sga.smk
@@ -1,25 +1,10 @@
-def get_sga_path() -> Path:
-    for fp in sys.path:
-        if fp.split("/")[-1] == "sbx_sga":
-            return Path(fp)
-    raise Error(
-        "Filepath for sbx_sga not found, are you sure it's installed under extensions/sbx_sga?"
-    )
-
-
 ISOLATE_FP = Cfg["all"]["output_fp"] / "isolate"
-SBX_SBA_VERSION = open(get_sga_path() / "VERSION").read().strip()
 TOOLS = ["shovill", "mlst", "checkm", "amr", "bakta", "mash"]
-
-
 try:
-    BENCHMARK_FP
+    SBX_SBA_VERSION = get_ext_version("sbx_sga")
 except NameError:
-    BENCHMARK_FP = output_subdir(Cfg, "benchmarks")
-try:
-    LOG_FP
-except NameError:
-    LOG_FP = output_subdir(Cfg, "logs")
+    # For backwards compatibility with older versions of Sunbeam
+    SBX_SBA_VERSION = "unknown"
 
 
 localrules:
@@ -70,7 +55,7 @@ rule sga_mash:
         zcat  {input.reads} > {output.agg}
         mash screen -w -p 8 {params.ref} {output.agg} > {output.win} 2> {log}
         sort -gr {output.win} > {output.sort} 2>> {log}
-    """
+        """
 
 
 rule sga_shovill: