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3130e92395
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0c1ba0470b
7 changed files with 1 additions and 274 deletions
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style="blue"
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28
.gitignore
vendored
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.gitignore
vendored
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!.vscode/settings.json
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!.vscode/tasks.json
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!.vscode/launch.json
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!.vscode/extensions.json
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### Julia gitignore ###
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## Files generated by invoking Julia with --code-coverage
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*.jl.cov
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*.jl.*.cov
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# Files generated by invoking Julia with --track-allocation
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*.jl.mem
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# System-specific files and directories generated by the BinaryProvider and BinDeps packages
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# They contain absolute paths specific to the host computer, and so should not be committed
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deps/deps.jl
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deps/build.log
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deps/downloads/
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deps/usr/
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deps/src/
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# Build artifacts for creating documentation generated by the Documenter package
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docs/build/
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docs/site/
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# File generated by Pkg, the package manager, based on a corresponding Project.toml
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# It records a fixed state of all packages used by the project. As such, it should not be
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# committed for packages, but should be committed for applications that require a static
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# environment.
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Manifest.toml
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!.vscode/extensions.json
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35
Project.toml
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Project.toml
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name = "Cowcalf_rumen_metagenomic_pipeline"
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uuid = "7d0d08ee-6932-474e-8e49-cd3f4679ce2d"
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authors = ["Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com> and contributors"]
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version = "0.1.0"
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[deps]
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CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
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Conda = "8f4d0f93-b110-5947-807f-2305c1781a2d"
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Cowsay = "b6370f49-8ad1-4651-ad9e-3639b35da0e9"
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Dagger = "d58978e5-989f-55fb-8d15-ea34adc7bf54"
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DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
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Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
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Glob = "c27321d9-0574-5035-807b-f59d2c89b15c"
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HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3"
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URIs = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4"
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YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
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[compat]
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CSV = "0.10.15"
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Conda = "1.10.2"
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Cowsay = "1.0.0"
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Dagger = "0.18.14"
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DataFrames = "1.7.0"
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Distributed = "1.11.0"
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Glob = "1.3.1"
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HTTP = "1.10.16"
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URIs = "1.5.2"
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YAML = "0.4.13"
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julia = "1.11"
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[extras]
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Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
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[targets]
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test = ["Test"]
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@ -1,8 +0,0 @@
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channels:
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- bioconda
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- conda-forge
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dependencies:
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- metaxa=2.2
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- blast-legacy=2.2.26
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- hmmer=3.1
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- mafft=7.525
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@ -1,90 +0,0 @@
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module Cowcalf_rumen_metagenomic_pipeline
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using Conda: Conda, runconda
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using Cowsay: cowsay
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using CSV: CSV
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using DataFrames: DataFrame, rename!
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using Distributed: pmap, @everywhere
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using Glob: GlobMatch, glob
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using HTTP: HTTP
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using URIs: URI
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using YAML: YAML
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export main
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include("Metaxa.jl")
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using .Metaxa: Metaxa
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_fetch_yaml_contents(yaml::AbstractString) = YAML.load_file(yaml)
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_fetch_yaml_contents(yaml::URI) = YAML.load(String(HTTP.get(yaml).body))
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function setup_remote_conda_environment(yaml::Union{AbstractString,URI}, env_name::Symbol)
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ENV["CONDA_JL_USE_MINIFORGE"] = "1"
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# Install x86 packages via Rosetta2 on MacOS
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if Sys.isapple()
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ENV["CONDA_SUBDIR"] = "osx-64"
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runconda(`config --env --set subdir osx-64`, env_name)
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end #if
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conda_definition = _fetch_yaml_contents(yaml)
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map(c -> Conda.add_channel(c, env_name), conda_definition["channels"])
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Conda.add(conda_definition["dependencies"], env_name)
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return env_name
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end #function
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function import_metadata(metadata_tsv::AbstractString)
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df = DataFrame(CSV.File(metadata_tsv))
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rename!(df, 1 => :sample_name)
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return df
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end #function
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function sample_files(samplenames::Vector{<:AbstractString})
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function _s(samplename::AbstractString)
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# Use explicit GlobMatch constructor b/c we need to interpolate values
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return (
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samplename,
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(
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abspath(first(glob(GlobMatch("$(samplename)*1*.fastq.gz")))),
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abspath(first(glob(GlobMatch("$(samplename)*2*.fastq.gz")))),
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),
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)
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end #function
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return map(_s, samplenames)
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end #function
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function (@main)(ARGS)
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metadata_file = pop!(ARGS)
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setup_remote_conda_environment(
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URI(
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"https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2024.10-py310-osx-conda.yml",
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),
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:qiime2,
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)
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setup_remote_conda_environment(
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joinpath(@__DIR__, "..", "conda_envs", "metaxa2.yml"),
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:metaxa2,
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)
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metadata = import_metadata(metadata_file)
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fastq_files = sample_files(metadata[!, :sample_name])
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@eval begin
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@everywhere begin
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include(joinpath(@__DIR__, "Metaxa.jl"))
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using .Metaxa: Metaxa
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end #@everywhere
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end #@eval
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taxonomy_files = pmap(x -> Metaxa.taxonomy(first(x), last(x)), fastq_files)
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feature_table = Metaxa.data_collector(taxonomy_files...)
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cp(feature_table, pwd())
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cowsay("Hello from Cowcalf_rumen_metagenomic_pipeline")
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return 0
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end #function
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end #module
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module Metaxa
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using Conda: runconda
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include("ProcessHelper.jl")
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using .ProcessHelper: exec_in_temp_dir
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export taxonomy
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function _classifier(
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samplename::AbstractString,
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fastq1::AbstractString,
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fastq2::AbstractString,
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)
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runconda(
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`run metaxa2 \
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-1 $fastq1 \
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-2 $fastq2 \
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-o $samplename \
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--format fastq \
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--cpu 4 \
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--summary F \
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--graphical F \
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--fasta F \
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--taxonomy T
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`,
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:metaxa2,
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)
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ispath("$samplename.taxonomy.txt") ||
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error("metaxa2 ran, but $samplename.taxonomy.txt was not found!")
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return abspath("$samplename.taxonomy.txt")
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end #function
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function _taxonomy_traversal(samplename::AbstractString, taxonomy::AbstractString)
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runconda(
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`run metaxa2_ttt \
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-i $taxonomy \
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-o $samplename \
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-m 7 \
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-n 7 \
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--summary F
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`,
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:metaxa2,
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)
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ispath("$samplename.level_7.txt") ||
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error("metaxa2 ran, but $samplename.level_7.txt was not found!")
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return abspath("$samplename.level_7.txt")
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end #function
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function taxonomy(
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samplename::AbstractString,
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fastq::Tuple{<:AbstractString,<:AbstractString},
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)
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taxonomy_file = exec_in_temp_dir(_classifier, samplename, fastq...)
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level_7_taxonomy_file = exec_in_temp_dir(_taxonomy_traversal, samplename, taxonomy_file)
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return level_7_taxonomy_file
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end #function
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function _dc(taxonomies::AbstractString...)
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runconda(
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`metaxa2_dc \
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-o feature-table.tsv \
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$(join(taxonomies, ' '))
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`,
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:metaxa2,
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)
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ispath("feature-table.tsv") ||
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error("metaxa2 ran, but feature-table.tsv was not found!")
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return abspath("feature-table.tsv")
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end #function
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function data_collector(taxonomies::AbstractString...)
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return exec_in_temp_dir(_dc, taxonomies...)
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end #function
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end #module
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module ProcessHelper
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export sym_temp
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"""
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sym_temp(file::AbstractString) -> (tmp_dir, link)
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sym_temp(files::Tuple{<:AbstractString,<:AbstractString}) -> (tmp_dir, links)
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Copies `file(s)` to a new temporary directory named `tmp_dir` and symbolically links them
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inside of that directory. Returns a tuple of the directory path and the path to the links.
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"""
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function sym_temp(files::AbstractString...)
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tmp_dir = mktempdir(; cleanup = false)
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@info "Creating temporary directory $tmp_dir"
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function _symlink(file::AbstractString)
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symlink_path = joinpath(tmp_dir, basename(file))
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symlink(realpath(file), symlink_path)
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@info "Symlinked $file to $symlink_path"
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return symlink_path
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end #function
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return (tmp_dir, map(_symlink, files))
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end #function
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function exec_in_temp_dir(f::Function, samplename::AbstractString, files::AbstractString...)
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tmp_dir, tmp_files = sym_temp(files...)
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return cd(() -> f(samplename, tmp_files...), tmp_dir)
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end #function
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function exec_in_temp_dir(f::Function, files::AbstractString...)
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tmp_dir, tmp_files = sym_temp(files...)
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return cd(() -> f(tmp_files...), tmp_dir)
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end #function
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end #module
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