# THIS FILE IS AUTOMATICALLY GENERATED BY CARGO
#
# When uploading crates to the registry Cargo will automatically
# "normalize" Cargo.toml files for maximal compatibility
# with all versions of Cargo and also rewrite `path` dependencies
# to registry (e.g., crates.io) dependencies.
#
# If you are reading this file be aware that the original Cargo.toml
# will likely look very different (and much more reasonable).
# See Cargo.toml.orig for the original contents.

[package]
edition = "2021"
name = "scrubby"
version = "0.4.0"
authors = ["esteinig <eike.steinig@unimelb.edu.au>"]
build = false
include = [
    "**/*.rs",
    "src/data/*",
    "Cargo.toml",
]
autobins = false
autoexamples = false
autotests = false
autobenches = false
description = "Remove or extract background taxa for metagenomic diagnostic applications"
homepage = "https://github.com/esteinig/scrubby"
documentation = "https://github.com/esteinig/scrubby"
readme = "README.md"
keywords = [
    "meta-gp",
    "scrubby",
    "cerebro",
    "host",
    "depletion",
]
categories = ["science"]
license = "MIT"
repository = "https://github.com/esteinig/scrubby"

[lib]
name = "scrubby"
path = "src/lib.rs"

[[bin]]
name = "scrubby"
path = "src/main.rs"

[dependencies.anstyle]
version = "1.0.7"

[dependencies.anyhow]
version = "1.0.86"

[dependencies.chrono]
version = "0.4.38"

[dependencies.clap]
version = "4.5.10"
features = [
    "derive",
    "unstable-styles",
    "cargo",
]

[dependencies.crossbeam]
version = "0.8.4"
optional = true

[dependencies.csv]
version = "1.3.0"

[dependencies.env_logger]
version = "0.11.4"

[dependencies.log]
version = "0.4.22"

[dependencies.minimap2]
version = "0.1.20"
optional = true

[dependencies.needletail]
version = "0.5.1"

[dependencies.niffler]
version = "2.5.0"

[dependencies.rand]
version = "0.8.5"
optional = true

[dependencies.rayon]
version = "1.10.0"

[dependencies.reqwest]
version = "0.12.5"
features = [
    "blocking",
    "native-tls-vendored",
]

[dependencies.rust-htslib]
version = "0.47.0"
optional = true

[dependencies.serde]
version = "1.0.204"
features = ["derive"]

[dependencies.serde_json]
version = "1.0.121"

[dependencies.tar]
version = "0.4.41"

[dependencies.tch]
version = "0.16.0"
optional = true

[dependencies.tempfile]
version = "3.10.1"

[dependencies.termcolor]
version = "1.4.1"

[dependencies.thiserror]
version = "1.0.63"

[features]
default = []
htslib = ["rust-htslib"]
mm2 = [
    "minimap2",
    "crossbeam",
]
nn = [
    "tch",
    "rand",
]