diff --git a/.circleci/config.yml b/.circleci/config.yml
index d575bd62..2ae5674e 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -6,7 +6,7 @@ version: 2
 jobs:
   build:
     docker:
-      - image: cimg/python:3.10
+      - image: continuumio/miniconda3
 
     steps:
       - checkout
diff --git a/.github/workflows/check_conda_envs.yml b/.github/workflows/check_conda_envs.yml
new file mode 100755
index 00000000..d1879f3c
--- /dev/null
+++ b/.github/workflows/check_conda_envs.yml
@@ -0,0 +1,27 @@
+name: Check Conda Envs
+
+on:
+  pull_request:
+    branches: [main]
+  push:
+    branches: [main]
+  workflow_dispatch:
+    inputs:
+      envs:
+        description: 'Regex for envs'     
+        required: false
+        default: './,workflow/envs/'
+
+jobs:
+  check_conda_envs:
+    name: Check Conda Envs
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v3
+      
+      - name: Check Conda Envs
+        uses: Ulthran/conda_env_check@v0
+        with:
+          envs: "./,workflow/envs/"
diff --git a/MANIFEST.in b/MANIFEST.in
index 6ee0cab1..d3fc5818 100755
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,2 +1,2 @@
-include sunbeamlib/data/*.yml
-include sunbeamlib/data/*.yaml
\ No newline at end of file
+include src/sunbeamlib/*.yml
+include src/sunbeamlib/*.yaml
\ No newline at end of file
diff --git a/Readme.md b/README.md
similarity index 83%
rename from Readme.md
rename to README.md
index 912539cb..210630e8 100644
--- a/Readme.md
+++ b/README.md
@@ -2,7 +2,11 @@
 
 # Sunbeam: a robust, extensible metagenomic sequencing pipeline 
 
-[![CircleCI](https://circleci.com/gh/sunbeam-labs/sunbeam/tree/main.svg?style=shield)](https://circleci.com/gh/sunbeam-labs/sunbeam/tree/main) [![Super-Linter](https://github.com/sunbeam-labs/sunbeam/actions/workflows/linter.yml/badge.svg)](https://github.com/sunbeam-labs/sunbeam/actions/workflows/linter.yml) [![Documentation Status](https://readthedocs.org/projects/sunbeam/badge/?version=stable)](https://sunbeam.readthedocs.io/en/stable/?badge=stable) [![DOI:10.1186/s40168-019-0658-x](https://img.shields.io/badge/Published%20in-Microbiome-1abc9c.svg)](https://doi.org/10.1186/s40168-019-0658-x)
+[![CircleCI](https://circleci.com/gh/sunbeam-labs/sunbeam/tree/main.svg?style=shield)](https://circleci.com/gh/sunbeam-labs/sunbeam/tree/main)
+[![Super-Linter](https://github.com/sunbeam-labs/sunbeam/actions/workflows/linter.yml/badge.svg)](https://github.com/sunbeam-labs/sunbeam/actions/workflows/linter.yml)
+[![Conda Envs Status](https://byob.yarr.is/sunbeam-labs/sunbeam/env_check)](https://github.com/sunbeam-labs/sunbeam/actions/workflows/check_conda_envs.yml)
+[![Documentation Status](https://readthedocs.org/projects/sunbeam/badge/?version=stable)](https://sunbeam.readthedocs.io/en/stable/?badge=stable)
+[![DOI:10.1186/s40168-019-0658-x](https://img.shields.io/badge/Published%20in-Microbiome-1abc9c.svg)](https://doi.org/10.1186/s40168-019-0658-x)
 
 Sunbeam is a pipeline written in [snakemake](http://snakemake.readthedocs.io)
 that simplifies and automates many of the steps in metagenomic sequencing
diff --git a/dev_scripts/reformat.sh b/dev_scripts/reformat.sh
index fe0627c3..289244ab 100755
--- a/dev_scripts/reformat.sh
+++ b/dev_scripts/reformat.sh
@@ -5,4 +5,4 @@ cd $SUNBEAM_DIR
 snakefmt workflow/rules/
 snakefmt workflow/Snakefile
 
-black workflow/scripts/ sunbeamlib/ tests/
+black workflow/scripts/ src/sunbeamlib/ tests/e2e/*.py tests/unit/rules/*.py tests/unit/sunbeamlib/*.py tests/*.py
diff --git a/docs/install.rst b/docs/install.rst
index 45846cfa..6298859d 100755
--- a/docs/install.rst
+++ b/docs/install.rst
@@ -48,14 +48,6 @@ code under the 'sunbeamlib/' directory. If you have major or incompatible
 changes to make to the environment you should consider creating a new one under a 
 different name so that you always have a working version installed.
 
--m/--no_mamba
-++++++++++++++++
-
-Don't use mamba in base environment as dependency solver. It is the default 
-option to use mamba because it is considerably faster than conda in solving new 
-environments. However it can also sometimes be a pain to install, especially 
-with crowded 'base' environments.
-
 -v/--verbose
 +++++++++++++++
 
diff --git a/environment.yml b/environment.yml
index 59c9a6f5..e3346ba9 100644
--- a/environment.yml
+++ b/environment.yml
@@ -3,7 +3,5 @@ channels:
   - bioconda
 dependencies:
   - snakemake
-  - ruamel.yaml
-  - semantic_version
   - git # Ensure sunbeam extend works even with tar installation of main pipeline
   - python>=3.10
diff --git a/install.sh b/install.sh
index cf6dba27..d4175ea5 100755
--- a/install.sh
+++ b/install.sh
@@ -9,7 +9,6 @@ read -r -d '' __usage <<-'EOF'
   -s --sunbeam_dir  [arg] Location of Sunbeam source code. Default: this directory
   -c --conda  [arg]       Location of Conda installation. Default: $CONDA_PREFIX
   -u --update [arg]       Update sunbeam [lib]rary, conda [env], or [all].
-  -m --no_mamba           Don't use mamba in base environment as dependency solver.
   -v --verbose            Show subcommand output.
   -d --debug              Run in debug mode.
   -h --help               Display this message and exit.
@@ -67,7 +66,6 @@ __sunbeam_dir="${arg_s:-$(readlink -f ${__dir})}"
 __sunbeam_env="${arg_e:-sunbeam${__version_tag}}"
 __update_lib=false
 __update_env=false
-__install_mamba=true
 if [[ "${arg_u}" = "all" || "${arg_u}" = "env" ]]; then
     __update_lib=true
     __update_env=true
@@ -75,10 +73,6 @@ elif [[ "${arg_u}" = "lib" ]]; then
     __update_lib=true
 fi
 
-if [[ "${arg_m:?}" = "1" ]]; then
-    __install_mamba=false
-fi
-
 __old_path=$PATH
 PATH=$PATH:${__conda_path}/bin
 
@@ -94,10 +88,6 @@ function __test_conda() {
     command -v conda &> /dev/null && echo true || echo false
 }
 
-function __test_mamba() {
-    command -v mamba &> /dev/null && echo true || echo false
-}
-
 function __detect_conda_install() {
     local discovered=$(__test_conda)
     if [[ $discovered = true ]]; then
@@ -160,12 +150,7 @@ function install_conda () {
 }
 
 function install_environment () {
-    if [[ $(__test_mamba) = true ]]; then
-        cmd=mamba
-    else
-        cmd=conda
-    fi
-    debug_capture $cmd env create --name=$__sunbeam_env \
+    debug_capture conda env create --name=$__sunbeam_env \
               --quiet --file environment.yml
     if [[ $(__test_env) != true ]]; then
 	installation_error "Environment creation"
@@ -198,8 +183,6 @@ info "    Sunbeam env:  '${__sunbeam_env}'"
 debug "Components detected:"
 __conda_installed=$(__test_conda)
 debug "    Conda:       ${__conda_installed}"
-__mamba_installed=$(__test_mamba)
-debug "    Mamba:       ${__mamba_installed}"
 __env_exists=$(__test_env)
 debug "    Environment: ${__env_exists}"
 __sunbeam_installed=$(__test_sunbeam)
@@ -221,16 +204,6 @@ else
     __env_changed=true
 fi
 
-# Install mamba
-if [[ $__mamba_installed = true ]]; then
-    info "Mamba already installed."
-else
-    if [[ $__install_mamba = true ]]; then
-        info "Installing mamba..."
-        conda install --yes --quiet -n base -c conda-forge mamba || (info "Mamba failed to install, this is usually because you have too many packages already installed to your base environment. Install again without mamba (--no_mamba) or try to fix conflicts in base env." && exit 1)
-    fi
-fi
-
 conda config --set channel_priority strict # Set channel priority on new install
 
 # Create Conda environment for Sunbeam
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100755
index 00000000..f89d7daf
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,160 @@
+[project]
+# This is the name of your project. The first time you publish this
+# package, this name will be registered for you. It will determine how
+# users can install this project, e.g.:
+#
+# $ pip install sampleproject
+#
+# And where it will live on PyPI: https://pypi.org/project/sampleproject/
+#
+# There are some restrictions on what makes a valid project name
+# specification here:
+# https://packaging.python.org/specifications/core-metadata/#name
+name = "sunbeamlib"  # Required
+
+# Versions should comply with PEP 440:
+# https://www.python.org/dev/peps/pep-0440/
+#
+# For a discussion on single-sourcing the version, see
+# https://packaging.python.org/guides/single-sourcing-package-version/
+#version = "0.0.0"  # Required
+dynamic = ["version"]
+
+# This is a one-line description or tagline of what your project does. This
+# corresponds to the "Summary" metadata field:
+# https://packaging.python.org/specifications/core-metadata/#summary
+description = "A helper package for running the sunbeam pipeline"  # Optional
+
+# This is an optional longer description of your project that represents
+# the body of text which users will see when they visit PyPI.
+#
+# Often, this is the same as your README, so you can just read it in from
+# that file directly (as we have already done above)
+#
+# This field corresponds to the "Description" metadata field:
+# https://packaging.python.org/specifications/core-metadata/#description-optional
+readme = "README.md" # Optional
+
+# Specify which Python versions you support. In contrast to the
+# 'Programming Language' classifiers above, 'pip install' will check this
+# and refuse to install the project if the version does not match. See
+# https://packaging.python.org/guides/distributing-packages-using-setuptools/#python-requires
+requires-python = ">=3.7"
+
+# This is either text indicating the license for the distribution, or a file
+# that contains the license
+# https://packaging.python.org/en/latest/specifications/core-metadata/#license
+# license = {file = "LICENSE.txt"}
+
+# This field adds keywords for your project which will appear on the
+# project page. What does your project relate to?
+#
+# Note that this is a list of additional keywords, separated
+# by commas, to be used to assist searching for the distribution in a
+# larger catalog.
+#keywords = ["bioinformatics", "metagenomics"]  # Optional
+
+# This should be your name or the name of the organization who originally
+# authored the project, and a valid email address corresponding to the name
+# listed.
+# authors = [
+#   {name = "A. Random Developer", email = "author@example.com" } # Optional
+# ]
+
+# This should be your name or the names of the organization who currently
+# maintains the project, and a valid email address corresponding to the name
+# listed.
+maintainers = [
+  {name = "Charlie Bushman", email = "ctbushman@gmail.com" } # Optional
+]
+
+# Classifiers help users find your project by categorizing it.
+#
+# For a list of valid classifiers, see https://pypi.org/classifiers/
+classifiers = [  # Optional
+  # How mature is this project? Common values are
+  #   3 - Alpha
+  #   4 - Beta
+  #   5 - Production/Stable
+  "Development Status :: 5 - Production/Stable",
+
+  # Indicate who your project is intended for
+  # "Intended Audience :: Developers",
+  #"Topic :: Bioinformatics",
+
+  # Pick your license as you wish
+  "License :: OSI Approved :: MIT License",
+
+  # Specify the Python versions you support here. In particular, ensure
+  # that you indicate you support Python 3. These classifiers are *not*
+  # checked by "pip install". See instead "python_requires" below.
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3.7",
+  "Programming Language :: Python :: 3.8",
+  "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3 :: Only",
+]
+
+# This field lists other packages that your project depends on to run.
+# Any package you put here will be installed by pip when your project is
+# installed, so they must be valid existing projects.
+#
+# For an analysis of this field vs pip's requirements files see:
+# https://packaging.python.org/discussions/install-requires-vs-requirements/
+dependencies = [ # Optional
+  "more-itertools",
+  "pyyaml",
+]
+
+# List additional groups of dependencies here (e.g. development
+# dependencies). Users will be able to install these using the "extras"
+# syntax, for example:
+#
+#   $ pip install sampleproject[dev]
+#
+# Similar to `dependencies` above, these must be valid existing
+# projects.
+[project.optional-dependencies] # Optional
+dev = ["black"]
+test = ["pytest"]
+
+# List URLs that are relevant to your project
+#
+# This field corresponds to the "Project-URL" and "Home-Page" metadata fields:
+# https://packaging.python.org/specifications/core-metadata/#project-url-multiple-use
+# https://packaging.python.org/specifications/core-metadata/#home-page-optional
+#
+# Examples listed include a pattern for specifying where the package tracks
+# issues, where the source is hosted, where to say thanks to the package
+# maintainers, and where to support the project financially. The key is
+# what's used to render the link text on PyPI.
+[project.urls]  # Optional
+"Homepage" = "https://github.com/sunbeam-labs/sunbeam"
+"Bug Reports" = "https://github.com/sunbeam-labs/sunbeam/issues"
+"Docs" = "https://sunbeam.readthedocs.io/en/stable/"
+# "Funding" = "https://donate.pypi.org"
+# "Say Thanks!" = "http://saythanks.io/to/example"
+"Source" = "https://github.com/sunbeam-labs/sunbeam"
+
+# The following would provide a command line executable called `sample`
+# which executes the function `main` from this package when invoked.
+[project.scripts]  # Optional
+sunbeam = "sunbeamlib.script_sunbeam:main"
+
+# This is configuration specific to the `setuptools` build backend.
+# If you are using a different build backend, you will need to change this.
+[tool.setuptools]
+# If there are data files included in your packages that need to be
+# installed, specify them here.
+#package-data = {"sunbeamlib" = ["*.yml", "*.yaml"]}
+
+[build-system]
+# These are the assumed default build requirements from pip:
+# https://pip.pypa.io/en/stable/reference/pip/#pep-517-and-518-support
+requires = ["setuptools>=61.0.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools.dynamic]
+version = {attr = "sunbeamlib.__version__"}
\ No newline at end of file
diff --git a/setup.py b/setup.py
deleted file mode 100644
index b19e5b66..00000000
--- a/setup.py
+++ /dev/null
@@ -1,16 +0,0 @@
-from setuptools import setup, find_packages
-
-setup(
-    name="sunbeam",
-    setup_requires=['setuptools'],
-    install_requires=['more-itertools', 'semantic_version', 'pytest'],
-    packages=find_packages(),
-    include_package_data=True,
-    package_data={"sunbeamlib": ["sunbeamlib/data/*.yml", "sunbeamlib/data/*.yaml"]},
-    entry_points={'console_scripts': [
-        'sunbeam = sunbeamlib.scripts.command:main'
-    ]},
-    classifiers=[
-        'Programming Language :: Python :: 3.9'
-    ]
-)
diff --git a/sunbeamlib/__init__.py b/src/sunbeamlib/__init__.py
similarity index 74%
rename from sunbeamlib/__init__.py
rename to src/sunbeamlib/__init__.py
index 277ce17d..f0adf88e 100755
--- a/sunbeamlib/__init__.py
+++ b/src/sunbeamlib/__init__.py
@@ -1,24 +1,47 @@
-__author__ = "Erik Clarke"
-__license__ = "GPL2+"
-
 import os
 import re
 import sys
 import csv
-
 from pathlib import Path
+from typing import Dict, List
 
-from semantic_version import Version
-from sunbeamlib.parse import parse_fasta
 
-__version__ = str(Version.coerce(os.environ.get("SUNBEAM_VER", "0.0.0")))
+class Version:
+    def __init__(self, version: str) -> None:
+        self.version = version
+        if self.version.startswith("v"):
+            self.version = self.version[1:]
 
+        version_parts = self.version.split(".")
+        self.major = version_parts[0]
+        try:
+            self.minor = version_parts[1]
+        except IndexError:
+            self.minor = 0
+        try:
+            self.patch = version_parts[2]
+        except IndexError:
+            self.patch = 0
+        if len(self.patch.split("-")) > 1:
+            self.patch = self.patch.split("-")[0]
 
-def load_sample_list(samplelist_fp, paired_end=True, root_proj=""):
+    def __str__(self) -> str:
+        return f"{self.major}.{self.minor}.{self.patch}"
+
+
+__version__ = str(Version(os.environ.get("SUNBEAM_VER", "0.0.0")))
+__author__ = "Erik Clarke"
+__license__ = "GPL2+"
+
+
+def load_sample_list(
+    samplelist_fp: Path, paired_end: bool = True
+) -> Dict[str, Dict[str, str]]:
     """
     Build a list of samples from a sample list file.
     :param samplelist_fp: a Path to a whitespace-delimited samplelist file,
        where the first entry is the sample name and the rest is ignored.
+    :param paired_end: if True, will look for a second column with mate pair
     :returns: A dictionary of samples with sample name and associated file(s)
     """
     Samples = {}
@@ -43,7 +66,9 @@ def load_sample_list(samplelist_fp, paired_end=True, root_proj=""):
     return Samples
 
 
-def guess_format_string(fnames, paired_end=True, split_pattern="([_.])"):
+def guess_format_string(
+    fnames: List[str], paired_end: bool = True, split_pattern: str = "([_.])"
+) -> str:
     """
     Try to guess the format string given a list of filenames.
     :param fnames: a list of filename strings
@@ -93,7 +118,7 @@ class SampleFormatError(Exception):
     pass
 
 
-def _verify_path(fp):
+def _verify_path(fp: str) -> str:
     if not fp:
         raise ValueError("Missing filename")
     path = Path(fp)
@@ -102,20 +127,13 @@ def _verify_path(fp):
     return str(path.resolve())
 
 
-def circular(seq, kmin, kmax, min_len):
+def circular(seq: str, kmin: int, kmax: int, min_len: int) -> bool:
     """Determine if a sequence is circular.
 
     Checks for repeated k-mer at beginning and end of a sequence for a given
-    range of values for k."""
+    range of values for k.
+    """
     if len(seq) < min_len:
         return False
     # Short-circuit checking: returns True for the first kmer that matches
     return any([k for k in range(kmin, kmax + 1) if seq[0:k] == seq[len(seq) - k :]])
-
-
-def read_seq_ids(fasta_fp):
-    """
-    Return the sequence identifiers for a given fasta filename.
-    """
-    with open(str(fasta_fp)) as f:
-        return list(parse_fasta(f))
diff --git a/sunbeamlib/config.py b/src/sunbeamlib/config.py
similarity index 66%
rename from sunbeamlib/config.py
rename to src/sunbeamlib/config.py
index bca8dd6d..7ac27565 100644
--- a/sunbeamlib/config.py
+++ b/src/sunbeamlib/config.py
@@ -1,19 +1,18 @@
 import os
 import sys
-from collections.abc import Mapping
+import yaml
 from pathlib import Path
 from pkg_resources import resource_stream
+from typing import Dict, TextIO, Tuple, Union
 
-from semantic_version import Version
-import ruamel.yaml
-from sunbeamlib import __version__
+from sunbeamlib import __version__, Version
 
 
-def makepath(path):
+def makepath(path: str) -> Path:
     return Path(path).expanduser()
 
 
-def verify(path):
+def verify(path: str) -> Path:
     path = Path(path)
     if path.exists():
         return path.resolve()
@@ -21,7 +20,7 @@ def verify(path):
         raise ValueError("Path %s does not exist" % path)
 
 
-def validate_paths(cfg, root):
+def validate_paths(cfg: Dict[str, str], root: Path) -> Dict[str, Union[str, Path]]:
     """Process paths in config file subsection.
 
     For each key ending in _fp, the value is:
@@ -31,6 +30,7 @@ def validate_paths(cfg, root):
     - expanded home directory ~
 
     :param cfg: a config file subsection
+    :param root: the root directory for the project
     :returns: an updated copy of cfg
     """
     new_cfg = dict()
@@ -51,7 +51,7 @@ def validate_paths(cfg, root):
     return new_cfg
 
 
-def check_compatibility(cfg):
+def check_compatibility(cfg: Dict[str, Dict[str, str]]) -> Tuple[str, str]:
     """Returns the major version numbers from the package and config file, respectively"""
 
     cfg_version = Version(cfg["all"].get("version", "0.0.0"))
@@ -60,7 +60,7 @@ def check_compatibility(cfg):
     return (pkg_version.major, cfg_version.major)
 
 
-def check_config(cfg):
+def check_config(cfg: Dict[str, Dict[str, str]]) -> Dict[str, Dict[str, str]]:
     """Resolve root in config file, then validate paths."""
 
     if "root" in cfg["all"]:
@@ -75,42 +75,37 @@ def check_config(cfg):
     return new_cfg
 
 
-def output_subdir(cfg, section):
+def output_subdir(cfg: Dict[str, Dict[str, str]], section: str) -> Path:
     return cfg["all"]["output_fp"] / cfg[section]["suffix"]
 
 
-def _update_dict(target, new):
+def _update_dict(
+    target: Dict[str, Union[str, Dict]], new: Dict[str, Union[str, Dict]]
+) -> Dict[str, Union[str, Dict]]:
     for k, v in new.items():
-        if isinstance(v, Mapping):
-            # We could use .get() here but ruamel.yaml's weird Mapping
-            # subclass outputs errors to stdout if the key doesn't exist
-            if k in target:
-                target[k] = _update_dict(target[k], v)
-            else:
-                target[k] = _update_dict({}, v)
+        if isinstance(v, dict):
+            target[k] = _update_dict(target.get(k, {}), v)
         else:
             target[k] = v
     return target
 
 
-def _update_dict_strict(target, new):
+def _update_dict_strict(
+    target: Dict[str, Union[str, Dict]], new: Dict[str, Union[str, Dict]]
+) -> Dict[str, Union[str, Dict]]:
     for k, v in new.items():
-        if isinstance(v, Mapping) and k in target.keys():
-            target[k] = _update_dict_strict(target.get(k, {}), v)
-        elif k in target.keys():
-            target[k] = v
-        else:
-            sys.stderr.write("Key '%s' not found in target, skipping\n" % k)
-            continue
+        target[k] = _update_dict_strict(target.get(k, {}), v)
     return target
 
 
-def update(config_str, new, strict=False):
-    config = ruamel.yaml.round_trip_load(config_str)
+def update(
+    config_str: str, new: Dict[str, Union[str, Dict]], strict: bool = False
+) -> Dict[str, Union[str, Dict]]:
+    config = yaml.safe_load(config_str)
     if strict:
         config = _update_dict_strict(config, new)
     else:
-        sbx_config = ruamel.yaml.round_trip_load(extension_config())
+        sbx_config = yaml.safe_load(extension_config())
         if sbx_config:
             for k, v in sbx_config.items():
                 if k not in config.keys():
@@ -120,12 +115,14 @@ def update(config_str, new, strict=False):
     return config
 
 
-def new(project_fp, version=__version__, template=None):
+def new(
+    project_fp: Union[str, Path], version: str = __version__, template: TextIO = None
+) -> str:
     if template:
         config = template.read()
     else:
         config = str(
-            resource_stream("sunbeamlib", "data/default_config.yml").read().decode()
+            resource_stream("sunbeamlib", "default_config.yml").read().decode()
         )
         # add config from extensions
         config = config + extension_config()
@@ -133,7 +130,7 @@ def new(project_fp, version=__version__, template=None):
     return config.format(PROJECT_FP=project_fp, SB_VERSION=version)
 
 
-def extension_config():
+def extension_config() -> str:
     config = ""
     sunbeam_dir = Path(os.getenv("SUNBEAM_DIR", os.getcwd()))
     for sbx in os.listdir(sunbeam_dir / "extensions"):
@@ -153,16 +150,14 @@ def extension_config():
     return config
 
 
-def load_defaults(default_name):
-    return ruamel.yaml.safe_load(
-        resource_stream("sunbeamlib", "data/{}.yml".format(default_name))
-        .read()
-        .decode()
+def load_defaults(default_name: str) -> Dict[str, Union[str, Dict]]:
+    return yaml.safe_load(
+        resource_stream("sunbeamlib", "{}.yml".format(default_name)).read().decode()
     )
 
 
-def dump(config, out=sys.stdout):
-    if isinstance(config, Mapping):
-        ruamel.yaml.round_trip_dump(config, out)
+def dump(config: Union[str, Dict], out: TextIO = sys.stdout) -> None:
+    if isinstance(config, dict):
+        yaml.safe_dump(config, out)
     else:
         out.write(config)
diff --git a/src/sunbeamlib/decontam.py b/src/sunbeamlib/decontam.py
new file mode 100755
index 00000000..85f59f86
--- /dev/null
+++ b/src/sunbeamlib/decontam.py
@@ -0,0 +1,31 @@
+from typing import Dict, Iterator, Tuple, Union
+
+from sunbeamlib.parse import parse_sam
+
+
+def get_mapped_reads(fp: str, min_pct_id: float, min_len_frac: float) -> Iterator[str]:
+    with open(fp, "r") as sam_file:
+        for read in parse_sam(sam_file):
+            if (
+                (not read["FLAG"] & 0x4)  # not unmapped
+                and (_get_frac(read) > min_len_frac)
+                and (_get_pct_identity(read) > min_pct_id)
+            ):
+                yield read["QNAME"]
+
+
+def _get_pct_identity(
+    read: Dict[str, Union[int, float, str, Tuple[int, str]]]
+) -> float:
+    edit_dist = read.get("NM", 0)
+    pct_mm = float(edit_dist) / len(read["SEQ"])
+    return 1 - pct_mm
+
+
+def _get_frac(read: Dict[str, Union[int, float, str, Tuple[int, str]]]) -> float:
+    clip = 0
+    for pair in read["CIGAR"]:
+        if pair[1] == "S" or pair[1] == "H":
+            clip += pair[0]
+    frac = float(len(read["SEQ"])) / (len(read["SEQ"]) + clip)
+    return frac
diff --git a/sunbeamlib/data/default_config.yml b/src/sunbeamlib/default_config.yml
similarity index 100%
rename from sunbeamlib/data/default_config.yml
rename to src/sunbeamlib/default_config.yml
diff --git a/sunbeamlib/data/default_profile.yaml b/src/sunbeamlib/default_profile.yaml
similarity index 100%
rename from sunbeamlib/data/default_profile.yaml
rename to src/sunbeamlib/default_profile.yaml
diff --git a/sunbeamlib/data/microb120.yml b/src/sunbeamlib/microb120.yml
similarity index 100%
rename from sunbeamlib/data/microb120.yml
rename to src/sunbeamlib/microb120.yml
diff --git a/src/sunbeamlib/parse.py b/src/sunbeamlib/parse.py
new file mode 100755
index 00000000..686f7bd3
--- /dev/null
+++ b/src/sunbeamlib/parse.py
@@ -0,0 +1,120 @@
+from itertools import groupby
+from more_itertools import grouper
+from pathlib import Path
+from typing import Dict, Iterator, List, TextIO, Tuple, Union
+
+
+BLAST6_DEFAULTS = [
+    "qseqid",
+    "sseqid",
+    "pident",
+    "length",
+    "mismatch",
+    "gapopen",
+    "qstart",
+    "qend",
+    "sstart",
+    "send",
+    "evalue",
+    "bitscore",
+]
+
+
+# Source: https://www.biostars.org/p/710/
+def parse_fasta(f: TextIO) -> Iterator[Tuple[str, str]]:
+    faiter = (x[1] for x in groupby(f, lambda line: line[0] == ">"))
+
+    for header in faiter:
+        # drop the ">"
+        header_str = header.__next__()[1:].strip()
+
+        # join all sequence lines to one.
+        seq_str = "".join(s.strip() for s in faiter.__next__())
+
+        yield (header_str, seq_str)
+
+
+def read_seq_ids(fasta_fp: Union[str, Path]) -> List[Tuple[str, str]]:
+    """
+    Return the sequence identifiers for a given fasta filepath.
+    """
+    with open(str(fasta_fp)) as f:
+        return list(parse_fasta(f))
+
+
+def write_fasta(record: Tuple[str, str], f: TextIO) -> None:
+    f.write(f">{record[0]}\n")
+    f.write(f"{record[1]}\n")
+
+
+def parse_fastq(f: TextIO) -> Iterator[Tuple[str, str, str, str]]:
+    for g in grouper(f.readlines(), 4):
+        header_str = g[0][1:].strip()
+        seq_str = g[1].strip()
+        plus_str = g[2].strip()
+        quality_str = g[3].strip()
+
+        yield (header_str, seq_str, plus_str, quality_str)
+
+
+def write_fastq(record: Tuple[str, str, str, str], f: TextIO) -> None:
+    for i, l in enumerate(record):
+        if i == 0:
+            f.write(f"@{l}\n")
+        else:
+            f.write(f"{l}\n")
+
+
+def write_many_fastq(record_list: List[Tuple[str, str, str, str]], f: TextIO) -> None:
+    record_list = [
+        [f"@{r[0]}\n", f"{r[1]}\n", f"{r[2]}\n", f"{r[3]}\n"] for r in record_list
+    ]
+    record_list = [item for sublist in record_list for item in sublist]
+    f.writelines(record_list)
+
+
+def parse_sam(
+    f: TextIO,
+) -> Iterator[Dict[str, Union[int, float, str, Tuple[int, str]]]]:
+    for line in f:
+        if line.startswith("@"):
+            continue
+
+        fields = line.strip().split("\t")
+        result = {
+            "QNAME": fields[0],
+            "FLAG": int(fields[1]),
+            "RNAME": fields[2],
+            "POS": int(fields[3]),
+            "MAPQ": int(fields[4]),
+            "CIGAR": fields[5],
+            "RNEXT": fields[6],
+            "PNEXT": int(fields[7]),
+            "TLEN": int(fields[8]),
+            "SEQ": fields[9],
+            "QUAL": fields[10],
+        }
+
+        cigar_tuples = []
+        current_length = "0"
+
+        for char in result["CIGAR"]:
+            if char.isdigit():
+                current_length += char
+            else:
+                cigar_tuples.append((int(current_length), char))
+                current_length = "0"
+
+        result["CIGAR"] = cigar_tuples
+
+        # Parse optional fields
+        optional_fields = fields[11:]
+        for field in optional_fields:
+            tag, data_type, value = field.split(":")
+            if data_type == "i":
+                value = int(value)
+            elif data_type == "f":
+                value = float(value)
+            result[tag] = value
+
+        yield result
diff --git a/sunbeamlib/data/pmacs.yml b/src/sunbeamlib/pmacs.yml
similarity index 100%
rename from sunbeamlib/data/pmacs.yml
rename to src/sunbeamlib/pmacs.yml
diff --git a/sunbeamlib/post.py b/src/sunbeamlib/post.py
similarity index 91%
rename from sunbeamlib/post.py
rename to src/sunbeamlib/post.py
index 402041ce..92754b15 100755
--- a/sunbeamlib/post.py
+++ b/src/sunbeamlib/post.py
@@ -3,7 +3,7 @@
 import os
 
 
-def compile_benchmarks(benchmark_fp: str, stats_fp: str):
+def compile_benchmarks(benchmark_fp: str, stats_fp: str) -> None:
     """Aggregate all the benchmark files into one and put it in stats_fp"""
     benchmarks = []
     try:
diff --git a/sunbeamlib/qc.py b/src/sunbeamlib/qc.py
similarity index 86%
rename from sunbeamlib/qc.py
rename to src/sunbeamlib/qc.py
index 49a91490..afc4c54e 100644
--- a/sunbeamlib/qc.py
+++ b/src/sunbeamlib/qc.py
@@ -3,10 +3,12 @@
 """
 
 import gzip
+from pathlib import Path
 from sunbeamlib.parse import parse_fastq, write_many_fastq
+from typing import List, TextIO
 
 
-def filter_ids(fp_in, fp_out, ids, log):
+def filter_ids(fp_in: Path, fp_out: Path, ids: List[str], log: TextIO) -> None:
     """Remove ids from FASTQ file.
 
     fp_in: path to input FASTQ
@@ -31,7 +33,7 @@ def filter_ids(fp_in, fp_out, ids, log):
         write_many_fastq(records, f_out)
 
 
-def remove_pair_id(id, log):
+def remove_pair_id(id: str, log: TextIO) -> str:
     """Remove the 1 or 2 from a paired read ID
 
     id: id string
diff --git a/sunbeamlib/reports.py b/src/sunbeamlib/reports.py
similarity index 81%
rename from sunbeamlib/reports.py
rename to src/sunbeamlib/reports.py
index bd0c2422..004958b0 100644
--- a/sunbeamlib/reports.py
+++ b/src/sunbeamlib/reports.py
@@ -1,13 +1,13 @@
-from collections import OrderedDict
+import pandas
 import re
 import os
 import sys
-
-import pandas
+from collections import OrderedDict
 from io import StringIO
+from typing import TextIO
 
 
-def parse_trim_summary_paired(f):
+def parse_trim_summary_paired(f: TextIO) -> OrderedDict[str, str]:
     for line in f.readlines():
         if line.startswith("Input Read"):
             vals = re.findall("\D+\: (\d+)", line)
@@ -15,7 +15,7 @@ def parse_trim_summary_paired(f):
             return OrderedDict(zip(keys, vals))
 
 
-def parse_trim_summary_single(f):
+def parse_trim_summary_single(f: TextIO) -> OrderedDict[str, str]:
     for line in f:
         if line.startswith("Input Read"):
             vals = re.findall("\D+\: (\d+)", line)
@@ -23,17 +23,19 @@ def parse_trim_summary_single(f):
             return OrderedDict(zip(keys, vals))
 
 
-def parse_decontam_log(f):
+def parse_decontam_log(f: TextIO) -> OrderedDict[str, str]:
     keys = f.readline().rstrip().split("\t")
     vals = f.readline().rstrip().split("\t")
     return OrderedDict(zip(keys, vals))
 
 
-def parse_komplexity_log(f):
-    return OrderedDict([("komplexity", len(f.readlines()))])
+def parse_komplexity_log(f: TextIO) -> OrderedDict[str, str]:
+    return OrderedDict([("komplexity", str(len(f.readlines())))])
 
 
-def summarize_qual_decontam(tfile, dfile, kfile, paired_end):
+def summarize_qual_decontam(
+    tfile: str, dfile: str, kfile: str, paired_end: bool
+) -> pandas.DataFrame:
     """Return a dataframe for summary information for trimmomatic and decontam rule"""
     tname = os.path.basename(tfile).split(".out")[0]
     with open(tfile) as tf:
@@ -56,7 +58,7 @@ def summarize_qual_decontam(tfile, dfile, kfile, paired_end):
     )
 
 
-def parse_fastqc_quality(filename):
+def parse_fastqc_quality(filename: str) -> pandas.DataFrame:
     with open(filename) as f:
         report = f.read()
     try:
diff --git a/sunbeamlib/scripts/_config.py b/src/sunbeamlib/script_config.py
similarity index 97%
rename from sunbeamlib/scripts/_config.py
rename to src/sunbeamlib/script_config.py
index 95e595f5..6f9998d1 100644
--- a/sunbeamlib/scripts/_config.py
+++ b/src/sunbeamlib/script_config.py
@@ -1,5 +1,5 @@
 import sys
-import ruamel.yaml
+import yaml
 import argparse
 
 from sunbeamlib import config
@@ -107,7 +107,7 @@ def update(args):
             "to prevent unexpected loss of config settings."
         )
 
-    old_config = ruamel.yaml.safe_load(args.config_file)
+    old_config = yaml.safe_load(args.config_file)
 
     # Remove the old version number
     old_config.get("all", {}).pop("version", None)
@@ -134,7 +134,7 @@ def update(args):
 
 def modify(args):
     update_src = args.str if args.str else args.file
-    new_values = ruamel.yaml.safe_load(update_src)
+    new_values = yaml.safe_load(update_src)
     if isinstance(new_values, str) and args.str:
         raise SystemExit(
             "Invalid YAML in --str. Did you make sure to put spaces between "
diff --git a/sunbeamlib/scripts/extend.py b/src/sunbeamlib/script_extend.py
similarity index 100%
rename from sunbeamlib/scripts/extend.py
rename to src/sunbeamlib/script_extend.py
diff --git a/sunbeamlib/scripts/init.py b/src/sunbeamlib/script_init.py
similarity index 97%
rename from sunbeamlib/scripts/init.py
rename to src/sunbeamlib/script_init.py
index b78df2eb..3279ccb7 100644
--- a/sunbeamlib/scripts/init.py
+++ b/src/sunbeamlib/script_init.py
@@ -2,10 +2,10 @@
 import shutil
 import sys
 import argparse
-import ruamel.yaml
+import yaml
 from pathlib import Path
 
-from .list_samples import (
+from sunbeamlib.script_list_samples import (
     build_sample_list,
     MissingMatePairError,
     SampleFormatError,
@@ -170,7 +170,7 @@ def write_config(args, project_fp, samplelists):
         cfg = config.new(project_fp=project_fp, template=args.template)
         defaults = {}
         if args.defaults:
-            defaults = ruamel.yaml.safe_load(args.defaults)
+            defaults = yaml.safe_load(args.defaults)
         # Override loaded config defaults (if any) for a few specific items.
         paired = layout == "paired"
         defaults["all"] = defaults.get("all", {})
@@ -189,7 +189,7 @@ def write_config(args, project_fp, samplelists):
 
 def write_profile(args, project_fp):
     sunbeam_dir = Path(os.getenv("SUNBEAM_DIR", os.getcwd()))
-    template_fp = sunbeam_dir / "sunbeamlib" / "data" / f"{args.profile}_profile.yaml"
+    template_fp = sunbeam_dir / "src" / "sunbeamlib" / f"{args.profile}_profile.yaml"
     config_fp = project_fp / "config.yaml"
     shutil.copyfile(template_fp, config_fp)
     with open(config_fp, "a") as f:
diff --git a/sunbeamlib/scripts/list_samples.py b/src/sunbeamlib/script_list_samples.py
similarity index 100%
rename from sunbeamlib/scripts/list_samples.py
rename to src/sunbeamlib/script_list_samples.py
diff --git a/sunbeamlib/scripts/run.py b/src/sunbeamlib/script_run.py
similarity index 88%
rename from sunbeamlib/scripts/run.py
rename to src/sunbeamlib/script_run.py
index 8868281c..99ded2f3 100644
--- a/sunbeamlib/scripts/run.py
+++ b/src/sunbeamlib/script_run.py
@@ -27,6 +27,12 @@ def main(argv=sys.argv):
         default=os.getenv("SUNBEAM_DIR", os.getcwd()),
         help="Path to Sunbeam installation",
     )
+    parser.add_argument(
+        "-m",
+        "--mamba",
+        action="store_true",
+        help="Use mamba instead of conda to manage environments",
+    )
     parser.add_argument(
         "--target_list", nargs="+", default=[], help="List of sunbeam targets"
     )
@@ -43,6 +49,8 @@ def main(argv=sys.argv):
 
     conda_prefix = Path(args.sunbeam_dir) / ".snakemake"
 
+    conda_cmd = "conda" if not args.mamba else "mamba"
+
     cmds = list()
     if args.target_list == []:
         args.target_list = [""]
@@ -61,6 +69,8 @@ def main(argv=sys.argv):
                 str(snakefile),
                 "--conda-prefix",
                 str(conda_prefix),
+                "--conda-frontend",
+                conda_cmd,
                 target,
             ]
             if arg
diff --git a/sunbeamlib/scripts/command.py b/src/sunbeamlib/script_sunbeam.py
similarity index 84%
rename from sunbeamlib/scripts/command.py
rename to src/sunbeamlib/script_sunbeam.py
index ef59e01b..f3b2e5fa 100644
--- a/sunbeamlib/scripts/command.py
+++ b/src/sunbeamlib/script_sunbeam.py
@@ -1,11 +1,12 @@
-import sys
 import argparse
+import sys
+
 import sunbeamlib
-from sunbeamlib.scripts.run import main as Run
-from sunbeamlib.scripts.init import main as Init
-from sunbeamlib.scripts._config import main as Config
-from sunbeamlib.scripts.list_samples import main as ListSamples
-from sunbeamlib.scripts.extend import main as Extend
+from sunbeamlib.script_run import main as Run
+from sunbeamlib.script_init import main as Init
+from sunbeamlib.script_config import main as Config
+from sunbeamlib.script_list_samples import main as ListSamples
+from sunbeamlib.script_extend import main as Extend
 
 
 def main():
diff --git a/sunbeamlib/data/slurm_profile.yaml b/src/sunbeamlib/slurm_profile.yaml
similarity index 100%
rename from sunbeamlib/data/slurm_profile.yaml
rename to src/sunbeamlib/slurm_profile.yaml
diff --git a/src/sunbeamlib/tibanna_profile.yaml b/src/sunbeamlib/tibanna_profile.yaml
new file mode 100755
index 00000000..d70ccd39
--- /dev/null
+++ b/src/sunbeamlib/tibanna_profile.yaml
@@ -0,0 +1,85 @@
+# Default options for running sunbeam on slurm
+rerun-incomplete: True
+rerun-triggers: "mtime"
+latency-wait: 90
+jobs: 10
+keep-going: True
+notemp: True
+printshellcmds: True
+nolock: True
+verbose: True
+use-conda: True
+cores: 24
+tibanna: True
+default-remote-prefix: ""
+
+
+# Default resource configuration
+default-resources:
+  - runtime=15
+  - mem_mb=8000
+  - disk_mb=1000
+# set-threads: map rule names to threads
+set-threads:
+  - diamond_reads=8
+  - gene_hits=8
+  - adapter_removal_unpaired=4
+  - adapter_removal_paired=4
+  - trimmomatic_unpaired=4
+  - trimmomatic_paired=4
+  - align_to_host=4
+  - kraken2_classify_report=8
+  - megahit_paired=4
+  - megahit_unpaired=4
+  - run_blastn=4
+  - run_diamond_blastp=4
+  - run_diamond_blastx=4
+  - align_to_genome=4
+  # - samtools_convert=4
+# set-resources: map rule names to resources in general
+set-resources:
+  - fq_2_fa:mem_mb=8000
+  - fq_2_fa:runtime=60
+  - build_gene_clusters_diamond_db:mem_mb=32000
+  - build_gene_clusters_diamond_db:runtime=30
+  - diamond_reads:mem_mb=32000
+  - diamond_reads:runtime=1440
+  - gene_hits:mem_mb=32000
+  - gene_hits:runtime=1440
+  - sample_intake:mem_mb=4000
+  - sample_intake:runtime=20
+  - adapter_removal_paired:mem_mb=8000
+  - adapter_removal_paired:runtime=60
+  - qc_final:mem_mb=8000
+  - qc_final:runtime=120
+  - demultiplex:mem_mb=10000
+  - demultiplex:runtime=720
+  - trimmomatic_paired:mem_mb=8000
+  - trimmomatic_paired:runtime=240
+  - fastqc:mem_mb=4000
+  - fastqc:runtime=120
+  - remove_low_complexity:mem_mb=32000
+  - remove_low_complexity:runtime=120
+  - align_to_host:mem_mb=16000
+  - align_to_host:runtime=240
+  - filter_unmapped_reads:mem_mb=24000
+  - filter_unmapped_reads:runtime=240
+  - megahit_paired:mem_mb=20000
+  - megahit_paired:runtime=720
+  - final_filter:mem_mb=4000
+  - kraken2_classify_report:mem_mb=48000
+  - kraken2_classify_report:runtime=2880
+  - kraken2_biom:mem_mb=4000
+  - kraken2_biom:runtime=240
+  - classic_k2_biom:mem_mb=4000
+  - classic_k2_biom:runtime=240
+  - run_blastn:mem_mb=16000
+  - run_blastn:runtime=720
+  - run_diamond_blastp:mem_mb=16000
+  - run_diamond_blastp:runtime=720
+  - run_diamond_blastx:mem_mb=24000
+  - run_diamond_blastx:runtime=720
+  - prodigal:mem_mb=16000
+  - prodigal:runtime=720
+  - aggregate_results:mem_mb=8000
+  - aggregate_results:runtime=120
\ No newline at end of file
diff --git a/sunbeamlib/decontam.py b/sunbeamlib/decontam.py
deleted file mode 100755
index 624ecf58..00000000
--- a/sunbeamlib/decontam.py
+++ /dev/null
@@ -1,31 +0,0 @@
-import pysam
-
-
-def get_mapped_reads(fp, min_pct_id, min_len_frac):
-    sam = pysam.AlignmentFile(fp)
-    for read in sam:
-        if (
-            (not read.is_unmapped)
-            and (_get_frac(read) > min_len_frac)
-            and (_get_pct_identity(read) > min_pct_id)
-        ):
-            yield read.query_name
-
-
-def _get_pct_identity(read):
-    if read.has_tag("NM"):
-        edit_dist = read.get_tag("NM")
-    else:
-        edit_dist = 0
-    pct_mm = float(edit_dist) / read.alen
-    return 1 - pct_mm
-
-
-def _get_frac(read):
-    cigar = read.cigartuples
-    clip = 0
-    for pair in cigar:
-        if pair[0] == 4 or pair[0] == 5:
-            clip = clip + pair[1]
-    frac = float(read.query_alignment_length) / (read.query_alignment_length + clip)
-    return frac
diff --git a/sunbeamlib/parse.py b/sunbeamlib/parse.py
deleted file mode 100755
index 28184795..00000000
--- a/sunbeamlib/parse.py
+++ /dev/null
@@ -1,70 +0,0 @@
-from itertools import groupby
-from more_itertools import grouper
-
-
-BLAST6_DEFAULTS = [
-    "qseqid",
-    "sseqid",
-    "pident",
-    "length",
-    "mismatch",
-    "gapopen",
-    "qstart",
-    "qend",
-    "sstart",
-    "send",
-    "evalue",
-    "bitscore",
-]
-
-
-# Source: https://www.biostars.org/p/710/
-def parse_fasta(f):
-    faiter = (x[1] for x in groupby(f, lambda line: line[0] == ">"))
-
-    for header in faiter:
-        # drop the ">"
-        header_str = header.__next__()[1:].strip()
-
-        # join all sequence lines to one.
-        seq_str = "".join(s.strip() for s in faiter.__next__())
-
-        yield (header_str, seq_str)
-
-
-def write_fasta(record, f):
-    f.write(f">{record[0]}\n")
-    f.write(f"{record[1]}\n")
-
-
-def parse_fastq(f):
-    for g in grouper(f.readlines(), 4):
-        header_str = g[0][1:].strip()
-        seq_str = g[1].strip()
-        plus_str = g[2].strip()
-        quality_str = g[3].strip()
-
-        yield (header_str, seq_str, plus_str, quality_str)
-
-
-def write_fastq(record, f):
-    for i, l in enumerate(record):
-        if i == 0:
-            f.write(f"@{l}\n")
-        else:
-            f.write(f"{l}\n")
-
-
-def write_many_fastq(record_list, f):
-    record_list = [
-        [f"@{r[0]}\n", f"{r[1]}\n", f"{r[2]}\n", f"{r[3]}\n"] for r in record_list
-    ]
-    record_list = [item for sublist in record_list for item in sublist]
-    f.writelines(record_list)
-
-
-def parse_blast6(f, outfmt=BLAST6_DEFAULTS):
-    for line in f.readlines():
-        vals = line.strip().split("\t")
-        if len(outfmt) == len(vals):
-            yield dict(zip(outfmt, vals))
diff --git a/sunbeamlib/scripts/__init__.py b/sunbeamlib/scripts/__init__.py
deleted file mode 100644
index e69de29b..00000000
diff --git a/tests/config_fixture.py b/tests/config_fixture.py
index e090d171..51d288e9 100755
--- a/tests/config_fixture.py
+++ b/tests/config_fixture.py
@@ -3,38 +3,32 @@
 import shutil
 import sys
 import tempfile
+import yaml
 from pathlib import Path
-from ruamel.yaml import YAML
 
 
 @pytest.fixture
 def config():
     tests_dir = Path(__file__).parent.resolve()
 
-    yaml = YAML(typ="safe")
     with open(tests_dir / "test_config.yml") as f:
-        config_dict = yaml.load(f)
-
-    if not shutil.which("mamba"):
-        sys.exit(
-            "Sunbeam needs mamba to be installed to run tests `conda install -c conda-forge mamba`. If you want to run sunbeam (not the tests) without mamba you can use `sunbeam run --profile /path/to/project/ --conda-frontend=conda`."
-        )
+        config_dict = yaml.safe_load(f)
 
     yield config_dict
 
 
 @pytest.fixture
 def output_dir(config):
-    yaml = config
+    config = config
     output_dir = Path()
 
-    if not yaml["output_dir"]:
+    if not config["output_dir"]:
         output_dir = Path(tempfile.mkdtemp())
     else:
-        output_dir = Path(yaml["output_dir"])
+        output_dir = Path(config["output_dir"])
         output_dir.mkdir(parents=True, exist_ok=True)
         if not os.listdir(output_dir) == []:
-            if yaml["overwrite"]:
+            if config["overwrite"]:
                 shutil.rmtree(output_dir)
                 output_dir.mkdir()
             else:
@@ -42,7 +36,7 @@ def output_dir(config):
                     "overwrite is set to false but output_dir points to a non-empty directory"
                 )
 
-    if not yaml["temp_env"]:
+    if not config["temp_env"]:
         pass
     else:
         # TODO: Create temp_env
@@ -67,5 +61,5 @@ def output_dir(config):
         shutil.move(extensions_moved_fp, extensions_fp)
     except FileNotFoundError as e:
         pass
-    if not yaml["output_dir"]:
+    if not config["output_dir"]:
         shutil.rmtree(output_dir)
diff --git a/tests/e2e/test_sunbeam_config.py b/tests/e2e/test_sunbeam_config.py
index 906eda58..caf932bd 100755
--- a/tests/e2e/test_sunbeam_config.py
+++ b/tests/e2e/test_sunbeam_config.py
@@ -3,8 +3,8 @@
 import shutil
 import subprocess as sp
 import sys
+import yaml
 from pathlib import Path
-from ruamel.yaml import YAML
 
 test_dir = Path(__file__).parent.parent.resolve()
 sys.path.append(test_dir)
@@ -58,9 +58,8 @@ def config_modify(init):
 def test_config_modify(config_modify):
     output_dir, hosts_fp = config_modify
 
-    yaml = YAML(typ="safe")
     with open(output_dir / "sunbeam_config.yml") as f:
-        config_dict = yaml.load(f)
+        config_dict = yaml.safe_load(f)
 
     assert config_dict["qc"]["host_fp"] == str(hosts_fp)
 
diff --git a/tests/unit/__init__.py b/tests/unit/__init__.py
deleted file mode 100755
index e69de29b..00000000
diff --git a/tests/unit/sunbeamlib/__init__.py b/tests/unit/sunbeamlib/__init__.py
deleted file mode 100755
index e69de29b..00000000
diff --git a/tests/unit/sunbeamlib/test__init__.py b/tests/unit/sunbeamlib/test__init__.py
index 3c11186b..2af759ee 100755
--- a/tests/unit/sunbeamlib/test__init__.py
+++ b/tests/unit/sunbeamlib/test__init__.py
@@ -14,7 +14,6 @@
     guess_format_string,
     _verify_path,
     circular,
-    read_seq_ids,
 )
 
 data_dir = Path(__file__).parent / "data"
diff --git a/tests/unit/sunbeamlib/test_parse.py b/tests/unit/sunbeamlib/test_parse.py
index a5f748c4..a0d1c1ee 100755
--- a/tests/unit/sunbeamlib/test_parse.py
+++ b/tests/unit/sunbeamlib/test_parse.py
@@ -1,7 +1,4 @@
 import gzip
-import os
-import pytest
-import shutil
 import sys
 from pathlib import Path
 
diff --git a/workflow/Snakefile b/workflow/Snakefile
index ad7e2bd2..962e74c8 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -17,8 +17,9 @@ from pathlib import Path, PurePath
 from snakemake.utils import update_config, listfiles
 from snakemake.exceptions import WorkflowError
 
-from sunbeamlib import load_sample_list, read_seq_ids
+from sunbeamlib import load_sample_list
 from sunbeamlib.config import *
+from sunbeamlib.parse import read_seq_ids
 from sunbeamlib.post import *
 from sunbeamlib.reports import *
 
@@ -74,7 +75,6 @@ for sbx in sbxs:
 Samples = load_sample_list(
     Cfg["all"]["samplelist_fp"],
     Cfg["all"]["paired_end"],
-    Cfg["all"]["root"] / Cfg["all"]["output_fp"],
 )
 Pairs = ["1", "2"] if Cfg["all"]["paired_end"] else ["1"]
 
diff --git a/workflow/envs/cutadapt.yml b/workflow/envs/cutadapt.yml
index fa062e41..2058827b 100755
--- a/workflow/envs/cutadapt.yml
+++ b/workflow/envs/cutadapt.yml
@@ -1,5 +1,7 @@
-name: cutadapt
 channels:
+  - conda-forge
   - bioconda
 dependencies:
-  - cutadapt
\ No newline at end of file
+  - cutadapt
+  - python =3.10.12
+name: cutadapt
diff --git a/workflow/envs/qc.yml b/workflow/envs/qc.yml
index 278e499a..a47f0781 100755
--- a/workflow/envs/qc.yml
+++ b/workflow/envs/qc.yml
@@ -1,9 +1,9 @@
-name: qc
-channels:
-  - bioconda
-  - conda-forge
-dependencies:
-  - bwa
-  - fastqc
-  - trimmomatic
-  - python>=3.10
\ No newline at end of file
+name: qc
+channels:
+  - bioconda
+  - conda-forge
+dependencies:
+  - bwa
+  - fastqc
+  - trimmomatic
+  - python =3.11.5
\ No newline at end of file
diff --git a/workflow/envs/samtools.linux-64.pin.txt b/workflow/envs/samtools.linux-64.pin.txt
deleted file mode 100644
index 8a3f3031..00000000
--- a/workflow/envs/samtools.linux-64.pin.txt
+++ /dev/null
@@ -1,40 +0,0 @@
-# This file may be used to create an environment using:
-# $ conda create --name <env> --file <this file>
-# platform: linux-64
-@EXPLICIT
-https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
-https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.7.22-hbcca054_0.conda#a73ecd2988327ad4c8f2c331482917f2
-https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.1.0-hfd8a6a1_0.conda#067bcc23164642f4c226da631f2a2e1d
-https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.10-3_cp310.conda#4eb33d14d794b0f4be116443ffed3853
-https://conda.anaconda.org/conda-forge/noarch/tzdata-2023c-h71feb2d_0.conda#939e3e74d8be4dac89ce83b20de2492a
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.1.0-he5830b7_0.conda#56ca14d57ac29a75d23a39eb3ee0ddeb
-https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.1.0-he5830b7_0.conda#cd93f779ff018dd85c7544c015c9db3c
-https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h7f98852_4.tar.bz2#a1fd65c7ccbf10880423d82bca54eb54
-https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.19.1-hd590300_0.conda#e8c18d865be43e2fb3f7a145b6adf1f5
-https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3
-https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.18-h0b41bf4_0.conda#6aa9c9de5542ecb07fdda9ca626252d8
-https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-h516909a_1.tar.bz2#6f8720dff19e17ce5d48cfe7f3d2f0a3
-https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3
-https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.0-h7f98852_0.tar.bz2#39b1328babf85c7c3a61636d9cd50206
-https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
-https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
-https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4-hcb278e6_0.conda#681105bccc2a3f7f1a837d47d39c9179
-https://conda.anaconda.org/conda-forge/linux-64/openssl-3.1.2-hd590300_0.conda#e5ac5227582d6c83ccf247288c0eb095
-https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
-https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
-https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.52.0-h61bc06f_0.conda#613955a50485812985c059e7b269f42e
-https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.42.0-h2797004_0.conda#fdaae20a1cf7cd62130a0973190a31b7
-https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.0-h0841786_0.conda#1f5a58e686b13bcfde88b93f547d23fe
-https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4
-https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.12-h27826a3_0.tar.bz2#5b8c42eb62e9fc961af70bdd6a26e168
-https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-hd590300_5.conda#68c34ec6149623be41a1933ab996a209
-https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.2-hfc55251_7.conda#32ae18eb2a687912fc9e92a501c0a11b
-https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.1-h659d440_0.conda#1b5126ec25763eb17ef74c8763d26e84
-https://conda.anaconda.org/conda-forge/linux-64/python-3.10.12-hd12c33a_0_cpython.conda#eb6f1df105f37daedd6dca78523baa75
-https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.2.1-hca28451_0.conda#96aec6156d58591f5a4e67056521ce1b
-https://conda.anaconda.org/conda-forge/noarch/setuptools-68.0.0-pyhd8ed1ab_0.conda#5a7739d0f57ee64133c9d32e6507c46d
-https://conda.anaconda.org/conda-forge/noarch/wheel-0.41.1-pyhd8ed1ab_0.conda#8f467ba2db2b5470d297953d9c1f9c7d
-https://conda.anaconda.org/conda-forge/noarch/pip-23.2.1-pyhd8ed1ab_0.conda#e2783aa3f9235225eec92f9081c5b801
-https://conda.anaconda.org/bioconda/linux-64/pysam-0.21.0-py310h41dec4a_1.tar.bz2#9af70a0f7f85e62d8262bcb3c439a7e8
diff --git a/workflow/envs/samtools.yml b/workflow/envs/samtools.yml
deleted file mode 100755
index 2ace65da..00000000
--- a/workflow/envs/samtools.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-name: samtools
-channels:
-  - conda-forge
-  - bioconda
-dependencies:
-  - pysam
-  - python>=3.10
\ No newline at end of file
diff --git a/workflow/rules/decontaminate.smk b/workflow/rules/decontaminate.smk
index 5f755e39..6c09fd53 100644
--- a/workflow/rules/decontaminate.smk
+++ b/workflow/rules/decontaminate.smk
@@ -60,8 +60,6 @@ rule get_mapped_reads:
     params:
         pct_id=Cfg["qc"]["pct_id"],
         frac=Cfg["qc"]["frac"],
-    conda:
-        "../envs/samtools.yml"
     script:
         "../scripts/get_mapped_reads.py"