diff --git a/.JuliaFormatter.toml b/.JuliaFormatter.toml
deleted file mode 100644
index 1e72b50..0000000
--- a/.JuliaFormatter.toml
+++ /dev/null
@@ -1 +0,0 @@
-style="blue"
diff --git a/.gitignore b/.gitignore
index f9c1b1b..3b1733d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,30 +2,4 @@
 !.vscode/settings.json
 !.vscode/tasks.json
 !.vscode/launch.json
-!.vscode/extensions.json
-
-### Julia gitignore ###
-## Files generated by invoking Julia with --code-coverage
-*.jl.cov
-*.jl.*.cov
-
-# Files generated by invoking Julia with --track-allocation
-*.jl.mem
-
-# System-specific files and directories generated by the BinaryProvider and BinDeps packages
-# They contain absolute paths specific to the host computer, and so should not be committed
-deps/deps.jl
-deps/build.log
-deps/downloads/
-deps/usr/
-deps/src/
-
-# Build artifacts for creating documentation generated by the Documenter package
-docs/build/
-docs/site/
-
-# File generated by Pkg, the package manager, based on a corresponding Project.toml
-# It records a fixed state of all packages used by the project. As such, it should not be
-# committed for packages, but should be committed for applications that require a static
-# environment.
-Manifest.toml
+!.vscode/extensions.json
\ No newline at end of file
diff --git a/Project.toml b/Project.toml
deleted file mode 100644
index ed6c11c..0000000
--- a/Project.toml
+++ /dev/null
@@ -1,35 +0,0 @@
-name = "Cowcalf_rumen_metagenomic_pipeline"
-uuid = "7d0d08ee-6932-474e-8e49-cd3f4679ce2d"
-authors = ["Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com> and contributors"]
-version = "0.1.0"
-
-[deps]
-CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
-Conda = "8f4d0f93-b110-5947-807f-2305c1781a2d"
-Cowsay = "b6370f49-8ad1-4651-ad9e-3639b35da0e9"
-Dagger = "d58978e5-989f-55fb-8d15-ea34adc7bf54"
-DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
-Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
-Glob = "c27321d9-0574-5035-807b-f59d2c89b15c"
-HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3"
-URIs = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4"
-YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
-
-[compat]
-CSV = "0.10.15"
-Conda = "1.10.2"
-Cowsay = "1.0.0"
-Dagger = "0.18.14"
-DataFrames = "1.7.0"
-Distributed = "1.11.0"
-Glob = "1.3.1"
-HTTP = "1.10.16"
-URIs = "1.5.2"
-YAML = "0.4.13"
-julia = "1.11"
-
-[extras]
-Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-
-[targets]
-test = ["Test"]
diff --git a/conda_envs/metaxa2.yml b/conda_envs/metaxa2.yml
deleted file mode 100644
index 4a27d02..0000000
--- a/conda_envs/metaxa2.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-channels:
-  - bioconda
-  - conda-forge
-dependencies:
-  - metaxa=2.2
-  - blast-legacy=2.2.26
-  - hmmer=3.1
-  - mafft=7.525
diff --git a/src/Cowcalf_rumen_metagenomic_pipeline.jl b/src/Cowcalf_rumen_metagenomic_pipeline.jl
deleted file mode 100644
index eba501a..0000000
--- a/src/Cowcalf_rumen_metagenomic_pipeline.jl
+++ /dev/null
@@ -1,90 +0,0 @@
-module Cowcalf_rumen_metagenomic_pipeline
-
-using Conda: Conda, runconda
-using Cowsay: cowsay
-using CSV: CSV
-using DataFrames: DataFrame, rename!
-using Distributed: pmap, @everywhere
-using Glob: GlobMatch, glob
-using HTTP: HTTP
-using URIs: URI
-using YAML: YAML
-
-export main
-
-include("Metaxa.jl")
-using .Metaxa: Metaxa
-
-_fetch_yaml_contents(yaml::AbstractString) = YAML.load_file(yaml)
-_fetch_yaml_contents(yaml::URI) = YAML.load(String(HTTP.get(yaml).body))
-
-function setup_remote_conda_environment(yaml::Union{AbstractString,URI}, env_name::Symbol)
-    ENV["CONDA_JL_USE_MINIFORGE"] = "1"
-
-    # Install x86 packages via Rosetta2 on MacOS
-    if Sys.isapple()
-        ENV["CONDA_SUBDIR"] = "osx-64"
-        runconda(`config --env --set subdir osx-64`, env_name)
-    end #if
-
-    conda_definition = _fetch_yaml_contents(yaml)
-
-    map(c -> Conda.add_channel(c, env_name), conda_definition["channels"])
-    Conda.add(conda_definition["dependencies"], env_name)
-
-    return env_name
-end #function
-
-function import_metadata(metadata_tsv::AbstractString)
-    df = DataFrame(CSV.File(metadata_tsv))
-    rename!(df, 1 => :sample_name)
-    return df
-end #function
-
-function sample_files(samplenames::Vector{<:AbstractString})
-    function _s(samplename::AbstractString)
-        # Use explicit GlobMatch constructor b/c we need to interpolate values
-        return (
-            samplename,
-            (
-                abspath(first(glob(GlobMatch("$(samplename)*1*.fastq.gz")))),
-                abspath(first(glob(GlobMatch("$(samplename)*2*.fastq.gz")))),
-            ),
-        )
-    end #function
-
-    return map(_s, samplenames)
-end #function
-
-function (@main)(ARGS)
-    metadata_file = pop!(ARGS)
-
-    setup_remote_conda_environment(
-        URI(
-            "https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2024.10-py310-osx-conda.yml",
-        ),
-        :qiime2,
-    )
-    setup_remote_conda_environment(
-        joinpath(@__DIR__, "..", "conda_envs", "metaxa2.yml"),
-        :metaxa2,
-    )
-
-    metadata = import_metadata(metadata_file)
-    fastq_files = sample_files(metadata[!, :sample_name])
-
-    @eval begin
-        @everywhere begin
-            include(joinpath(@__DIR__, "Metaxa.jl"))
-            using .Metaxa: Metaxa
-        end #@everywhere
-    end #@eval
-    taxonomy_files = pmap(x -> Metaxa.taxonomy(first(x), last(x)), fastq_files)
-    feature_table = Metaxa.data_collector(taxonomy_files...)
-    cp(feature_table, pwd())
-
-    cowsay("Hello from Cowcalf_rumen_metagenomic_pipeline")
-    return 0
-end #function
-
-end #module
diff --git a/src/Metaxa.jl b/src/Metaxa.jl
deleted file mode 100644
index 4b93d19..0000000
--- a/src/Metaxa.jl
+++ /dev/null
@@ -1,77 +0,0 @@
-module Metaxa
-
-using Conda: runconda
-
-include("ProcessHelper.jl")
-
-using .ProcessHelper: exec_in_temp_dir
-
-export taxonomy
-
-function _classifier(
-    samplename::AbstractString,
-    fastq1::AbstractString,
-    fastq2::AbstractString,
-)
-    runconda(
-        `run metaxa2 \
-            -1 $fastq1 \
-            -2 $fastq2 \
-            -o $samplename \
-            --format fastq \
-            --cpu 4 \
-            --summary F \
-            --graphical F \
-            --fasta F \
-            --taxonomy T
-        `,
-        :metaxa2,
-    )
-    ispath("$samplename.taxonomy.txt") ||
-        error("metaxa2 ran, but $samplename.taxonomy.txt was not found!")
-    return abspath("$samplename.taxonomy.txt")
-end #function
-
-function _taxonomy_traversal(samplename::AbstractString, taxonomy::AbstractString)
-    runconda(
-        `run metaxa2_ttt \
-            -i $taxonomy \
-            -o $samplename \
-            -m 7 \
-            -n 7 \
-            --summary F
-        `,
-        :metaxa2,
-    )
-    ispath("$samplename.level_7.txt") ||
-        error("metaxa2 ran, but $samplename.level_7.txt was not found!")
-    return abspath("$samplename.level_7.txt")
-end #function
-
-function taxonomy(
-    samplename::AbstractString,
-    fastq::Tuple{<:AbstractString,<:AbstractString},
-)
-    taxonomy_file = exec_in_temp_dir(_classifier, samplename, fastq...)
-    level_7_taxonomy_file = exec_in_temp_dir(_taxonomy_traversal, samplename, taxonomy_file)
-    return level_7_taxonomy_file
-end #function
-
-function _dc(taxonomies::AbstractString...)
-    runconda(
-        `metaxa2_dc \
-            -o feature-table.tsv \
-            $(join(taxonomies, ' '))
-        `,
-        :metaxa2,
-    )
-    ispath("feature-table.tsv") ||
-        error("metaxa2 ran, but feature-table.tsv was not found!")
-    return abspath("feature-table.tsv")
-end #function
-
-function data_collector(taxonomies::AbstractString...)
-    return exec_in_temp_dir(_dc, taxonomies...)
-end #function
-
-end #module
diff --git a/src/ProcessHelper.jl b/src/ProcessHelper.jl
deleted file mode 100644
index ca01370..0000000
--- a/src/ProcessHelper.jl
+++ /dev/null
@@ -1,36 +0,0 @@
-module ProcessHelper
-
-export sym_temp
-
-"""
-  sym_temp(file::AbstractString) -> (tmp_dir, link)
-  sym_temp(files::Tuple{<:AbstractString,<:AbstractString}) -> (tmp_dir, links)
-
-Copies `file(s)` to a new temporary directory named `tmp_dir` and symbolically links them
-inside of that directory. Returns a tuple of the directory path and the path to the links.
-"""
-function sym_temp(files::AbstractString...)
-    tmp_dir = mktempdir(; cleanup = false)
-    @info "Creating temporary directory $tmp_dir"
-
-    function _symlink(file::AbstractString)
-        symlink_path = joinpath(tmp_dir, basename(file))
-        symlink(realpath(file), symlink_path)
-        @info "Symlinked $file to $symlink_path"
-        return symlink_path
-    end #function
-
-    return (tmp_dir, map(_symlink, files))
-end #function
-
-function exec_in_temp_dir(f::Function, samplename::AbstractString, files::AbstractString...)
-    tmp_dir, tmp_files = sym_temp(files...)
-    return cd(() -> f(samplename, tmp_files...), tmp_dir)
-end #function
-
-function exec_in_temp_dir(f::Function, files::AbstractString...)
-    tmp_dir, tmp_files = sym_temp(files...)
-    return cd(() -> f(tmp_files...), tmp_dir)
-end #function
-
-end #module