From 9a91fed82f2e92be2eaf69b2cad73f252c4e3b3f Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Fri, 11 Apr 2025 09:27:43 -0500
Subject: [PATCH 1/4] feat: Bootstrap basic package

---
 .gitignore                                | 28 ++++++++++++++++++++++-
 Project.toml                              | 17 ++++++++++++++
 src/Cowcalf_rumen_metagenomic_pipeline.jl |  8 +++++++
 3 files changed, 52 insertions(+), 1 deletion(-)
 create mode 100644 Project.toml
 create mode 100644 src/Cowcalf_rumen_metagenomic_pipeline.jl

diff --git a/.gitignore b/.gitignore
index 3b1733d..f9c1b1b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,4 +2,30 @@
 !.vscode/settings.json
 !.vscode/tasks.json
 !.vscode/launch.json
-!.vscode/extensions.json
\ No newline at end of file
+!.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
diff --git a/Project.toml b/Project.toml
new file mode 100644
index 0000000..d25e064
--- /dev/null
+++ b/Project.toml
@@ -0,0 +1,17 @@
+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]
+Cowsay = "b6370f49-8ad1-4651-ad9e-3639b35da0e9"
+
+[compat]
+Cowsay = "1.0.0"
+julia = "1.11"
+
+[extras]
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["Test"]
diff --git a/src/Cowcalf_rumen_metagenomic_pipeline.jl b/src/Cowcalf_rumen_metagenomic_pipeline.jl
new file mode 100644
index 0000000..2aac62f
--- /dev/null
+++ b/src/Cowcalf_rumen_metagenomic_pipeline.jl
@@ -0,0 +1,8 @@
+module Cowcalf_rumen_metagenomic_pipeline
+    using Cowsay: cowsay
+
+    function main()
+        cowsay("Hello from Cowcalf_rumen_metagenomic_pipeline")
+        return 0
+    end #function
+end #module

From 81f49a8ad8fa9d125a7231eca54794c7ebd67198 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Fri, 11 Apr 2025 21:01:45 -0500
Subject: [PATCH 2/4] feat: Add Conda environment installer

---
 Project.toml                              |  8 ++++++++
 src/Cowcalf_rumen_metagenomic_pipeline.jl | 24 +++++++++++++++++++++++
 2 files changed, 32 insertions(+)

diff --git a/Project.toml b/Project.toml
index d25e064..9803d24 100644
--- a/Project.toml
+++ b/Project.toml
@@ -4,10 +4,18 @@ authors = ["Thomas A. Christensen II <25492070+MillironX@users.noreply.github.co
 version = "0.1.0"
 
 [deps]
+Conda = "8f4d0f93-b110-5947-807f-2305c1781a2d"
 Cowsay = "b6370f49-8ad1-4651-ad9e-3639b35da0e9"
+HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3"
+URIs = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4"
+YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
 
 [compat]
+Conda = "1.10.2"
 Cowsay = "1.0.0"
+HTTP = "1.10.16"
+URIs = "1.5.2"
+YAML = "0.4.13"
 julia = "1.11"
 
 [extras]
diff --git a/src/Cowcalf_rumen_metagenomic_pipeline.jl b/src/Cowcalf_rumen_metagenomic_pipeline.jl
index 2aac62f..6dc43fa 100644
--- a/src/Cowcalf_rumen_metagenomic_pipeline.jl
+++ b/src/Cowcalf_rumen_metagenomic_pipeline.jl
@@ -1,5 +1,29 @@
 module Cowcalf_rumen_metagenomic_pipeline
+    using Conda: Conda, runconda
     using Cowsay: cowsay
+    using HTTP: HTTP
+    using URIs: URI
+    using YAML: YAML
+
+    _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 main()
         cowsay("Hello from Cowcalf_rumen_metagenomic_pipeline")

From 9df8163123e79c39a23ef78571fa6226de961244 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Fri, 11 Apr 2025 21:05:13 -0500
Subject: [PATCH 3/4] style: Add formatter requirements

---
 .JuliaFormatter.toml                      |  1 +
 src/Cowcalf_rumen_metagenomic_pipeline.jl | 48 ++++++++++++-----------
 2 files changed, 26 insertions(+), 23 deletions(-)
 create mode 100644 .JuliaFormatter.toml

diff --git a/.JuliaFormatter.toml b/.JuliaFormatter.toml
new file mode 100644
index 0000000..1e72b50
--- /dev/null
+++ b/.JuliaFormatter.toml
@@ -0,0 +1 @@
+style="blue"
diff --git a/src/Cowcalf_rumen_metagenomic_pipeline.jl b/src/Cowcalf_rumen_metagenomic_pipeline.jl
index 6dc43fa..7218120 100644
--- a/src/Cowcalf_rumen_metagenomic_pipeline.jl
+++ b/src/Cowcalf_rumen_metagenomic_pipeline.jl
@@ -1,32 +1,34 @@
 module Cowcalf_rumen_metagenomic_pipeline
-    using Conda: Conda, runconda
-    using Cowsay: cowsay
-    using HTTP: HTTP
-    using URIs: URI
-    using YAML: YAML
 
-    _fetch_yaml_contents(yaml::AbstractString) = YAML.load_file(yaml)
-    _fetch_yaml_contents(yaml::URI) = YAML.load(String(HTTP.get(yaml).body))
+using Conda: Conda, runconda
+using Cowsay: cowsay
+using HTTP: HTTP
+using URIs: URI
+using YAML: YAML
 
-    function setup_remote_conda_environment(yaml::Union{AbstractString,URI}, env_name::Symbol)
-        ENV["CONDA_JL_USE_MINIFORGE"] = "1"
+_fetch_yaml_contents(yaml::AbstractString) = YAML.load_file(yaml)
+_fetch_yaml_contents(yaml::URI) = YAML.load(String(HTTP.get(yaml).body))
 
-        # 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
+function setup_remote_conda_environment(yaml::Union{AbstractString,URI}, env_name::Symbol)
+    ENV["CONDA_JL_USE_MINIFORGE"] = "1"
 
-        conda_definition = _fetch_yaml_contents(yaml)
+    # 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
 
-        map(c -> Conda.add_channel(c, env_name), conda_definition["channels"])
-        Conda.add(conda_definition["dependencies"], env_name)
+    conda_definition = _fetch_yaml_contents(yaml)
 
-        return env_name
-    end #function
+    map(c -> Conda.add_channel(c, env_name), conda_definition["channels"])
+    Conda.add(conda_definition["dependencies"], env_name)
+
+    return env_name
+end #function
+
+function main()
+    cowsay("Hello from Cowcalf_rumen_metagenomic_pipeline")
+    return 0
+end #function
 
-    function main()
-        cowsay("Hello from Cowcalf_rumen_metagenomic_pipeline")
-        return 0
-    end #function
 end #module

From 3130e92395724b9115854b3019678dad20615d4d Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Mon, 14 Apr 2025 11:12:41 -0500
Subject: [PATCH 4/4] feat: Add metaxa steps

---
 Project.toml                              | 10 +++
 conda_envs/metaxa2.yml                    |  8 +++
 src/Cowcalf_rumen_metagenomic_pipeline.jl | 58 ++++++++++++++++-
 src/Metaxa.jl                             | 77 +++++++++++++++++++++++
 src/ProcessHelper.jl                      | 36 +++++++++++
 5 files changed, 188 insertions(+), 1 deletion(-)
 create mode 100644 conda_envs/metaxa2.yml
 create mode 100644 src/Metaxa.jl
 create mode 100644 src/ProcessHelper.jl

diff --git a/Project.toml b/Project.toml
index 9803d24..ed6c11c 100644
--- a/Project.toml
+++ b/Project.toml
@@ -4,15 +4,25 @@ authors = ["Thomas A. Christensen II <25492070+MillironX@users.noreply.github.co
 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"
diff --git a/conda_envs/metaxa2.yml b/conda_envs/metaxa2.yml
new file mode 100644
index 0000000..4a27d02
--- /dev/null
+++ b/conda_envs/metaxa2.yml
@@ -0,0 +1,8 @@
+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
index 7218120..eba501a 100644
--- a/src/Cowcalf_rumen_metagenomic_pipeline.jl
+++ b/src/Cowcalf_rumen_metagenomic_pipeline.jl
@@ -2,10 +2,19 @@ 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))
 
@@ -26,7 +35,54 @@ function setup_remote_conda_environment(yaml::Union{AbstractString,URI}, env_nam
     return env_name
 end #function
 
-function main()
+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
diff --git a/src/Metaxa.jl b/src/Metaxa.jl
new file mode 100644
index 0000000..4b93d19
--- /dev/null
+++ b/src/Metaxa.jl
@@ -0,0 +1,77 @@
+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
new file mode 100644
index 0000000..ca01370
--- /dev/null
+++ b/src/ProcessHelper.jl
@@ -0,0 +1,36 @@
+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