diff --git a/.editorconfig b/.editorconfig new file mode 100644 index 0000000..101ca1d --- /dev/null +++ b/.editorconfig @@ -0,0 +1,27 @@ +# http://editorconfig.org + +root = true + +[*] +charset = utf-8 +end_of_line = lf +insert_final_newline = true +trim_trailing_whitespace = true + +[*.{py,rst,ini,rs,toml}] +indent_style = space +indent_size = 4 + +[*.{html,css,scss,json,yml}] +indent_style = space +indent_size = 2 + +[*.md] +trim_trailing_whitespace = false + +[Makefile] +indent_style = tab + +[nginx.conf] +indent_style = space +indent_size = 2 diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md new file mode 100644 index 0000000..0f38948 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/bug_report.md @@ -0,0 +1,46 @@ +--- +name: Bug report +about: Create a report to help us improve +title: '' +labels: bug +assignees: '' + +--- + + + +**Describe the bug** +A clear and concise description of what the bug is. + +**To Reproduce** +Steps to reproduce the behavior: +1. Go to '...' +2. Click on '....' +3. Scroll down to '....' +4. See error + +**Expected behavior** +A clear and concise description of what you expected to happen. + +**Screenshots** +If applicable, add screenshots to help explain your problem. + +**Desktop (please complete the following information):** + - OS: [e.g. iOS] + - Browser [e.g. chrome, safari] + - Version [e.g. 22] + +**Smartphone (please complete the following information):** + - Device: [e.g. iPhone6] + - OS: [e.g. iOS8.1] + - Browser [e.g. stock browser, safari] + - Version [e.g. 22] + +**Additional context** +Add any other context about the problem here. diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md new file mode 100644 index 0000000..609d5be --- /dev/null +++ b/.github/ISSUE_TEMPLATE/feature_request.md @@ -0,0 +1,28 @@ +--- +name: Feature request +about: Suggest an idea for this project +title: '' +labels: enhancement +assignees: '' + +--- + + + +**Is your feature request related to a problem? Please describe.** +A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] + +**Describe the solution you'd like** +A clear and concise description of what you want to happen. + +**Describe alternatives you've considered** +A clear and concise description of any alternative solutions or features you've considered. + +**Additional context** +Add any other context or screenshots about the feature request here. diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 0000000..62637fa --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,9 @@ +# Please see the documentation for all configuration options: +# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates + +version: 2 +updates: + - package-ecosystem: "cargo" + directory: "/" + schedule: + interval: "weekly" diff --git a/.github/workflows/automerge.yml b/.github/workflows/automerge.yml new file mode 100644 index 0000000..05c540d --- /dev/null +++ b/.github/workflows/automerge.yml @@ -0,0 +1,19 @@ +name: Dependabot auto-merge + +on: pull_request + +permissions: + contents: write + +jobs: + dependabot: + runs-on: ubuntu-latest + if: ${{ github.actor == 'dependabot[bot]' }} + steps: + - name: Enable auto-merge for Dependabot PRs + run: gh pr merge --auto --squash "$PR_URL" + env: + PR_URL: ${{github.event.pull_request.html_url}} + # GitHub provides this variable in the CI env. You don't + # need to add anything to the secrets vault. + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/conventional-prs.yml b/.github/workflows/conventional-prs.yml new file mode 100644 index 0000000..17c8812 --- /dev/null +++ b/.github/workflows/conventional-prs.yml @@ -0,0 +1,18 @@ +name: PR +on: + pull_request_target: + types: + - opened + - reopened + - edited + - synchronize + +jobs: + title-format: + runs-on: ubuntu-latest + steps: + - uses: amannn/action-semantic-pull-request@v3.4.0 + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + with: + validateSingleCommit: true diff --git a/.github/workflows/release-please.yml b/.github/workflows/release-please.yml new file mode 100644 index 0000000..c2a5b43 --- /dev/null +++ b/.github/workflows/release-please.yml @@ -0,0 +1,37 @@ +on: + push: + branches: + - main + +name: release-please + +jobs: + release-please: + if: github.repository_owner == 'bihealth' + runs-on: ubuntu-latest + steps: + - uses: GoogleCloudPlatform/release-please-action@v2 + id: release + with: + release-type: rust + package-name: scarus + + - uses: actions/checkout@v3 + if: ${{ steps.release.outputs.release_created }} + + - name: Install stable toolchain + uses: actions-rs/toolchain@v1 + if: ${{ steps.release.outputs.release_created }} + with: + toolchain: stable + override: true + + - uses: Swatinem/rust-cache@v2 + if: ${{ steps.release.outputs.release_created }} + + - name: Publish crate + if: ${{ steps.release.outputs.release_created }} + uses: actions-rs/cargo@v1 + with: + command: publish + args: --token ${{ secrets.CRATES_IO_TOKEN }} diff --git a/.github/workflows/rust.yml b/.github/workflows/rust.yml new file mode 100644 index 0000000..e8c8a70 --- /dev/null +++ b/.github/workflows/rust.yml @@ -0,0 +1,75 @@ +name: CI + +on: + push: + branches: + - main + pull_request: + branches: + - main + +jobs: + Formatting: + runs-on: ubuntu-latest + steps: + - name: Checkout repository + uses: actions/checkout@v3 + + - name: Install stable toolchain + uses: actions-rs/toolchain@v1 + with: + toolchain: stable + override: true + components: rustfmt + + - name: Check format + run: | + cargo fmt -- --check + + Linting: + runs-on: ubuntu-latest + steps: + - name: Checkout repository + uses: actions/checkout@v3 + + - name: Install stable toolchain + uses: actions-rs/toolchain@v1 + with: + toolchain: stable + override: true + components: clippy + + - name: Lint with clippy + uses: actions-rs/clippy-check@v1 + with: + token: ${{ secrets.GITHUB_TOKEN }} + + Testing: + needs: Formatting + runs-on: ubuntu-latest + steps: + - name: Checkout repository + uses: actions/checkout@v3 + with: + lfs: true + + - name: Install stable toolchain + uses: actions-rs/toolchain@v1 + with: + toolchain: stable + override: true + + - uses: Swatinem/rust-cache@v2 + + - name: Run cargo-tarpaulin + uses: actions-rs/tarpaulin@v0.1 + with: + version: 0.21.0 + args: "--skip-clean -- --test-threads 1" + + - name: Codecov + uses: codecov/codecov-action@v3 + with: + verbose: true + fail_ci_if_error: true + token: ${{ secrets.CODECOV_TOKEN }} diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..aeb027d --- /dev/null +++ b/.gitignore @@ -0,0 +1,6 @@ +/target +/Cargo.lock + +*~ +.*.sw? + diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 0000000..825c32f --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1 @@ +# Changelog diff --git a/Cargo.toml b/Cargo.toml new file mode 100644 index 0000000..fdf741d --- /dev/null +++ b/Cargo.toml @@ -0,0 +1,33 @@ +[package] +name = "scarus" +version = "0.1.0" +edition = "2021" +authors = ["Manuel Holtgrewe "] +description = "Automated evaluation of ACMG rules" +license = "MIT" +homepage = "https://github.com/bihealth/scarus" +readme = "README.md" + +[[bin]] +name = "scarus" +path = "src/main.rs" + +[dependencies] +anyhow = "1.0" +clap-verbosity-flag = "2.0" +clap = { version = "4.4", features = ["derive", "help"] } +log = "0.4" +thiserror = "1.0" +tokio = { version = "1.33", features = ["full"] } +tracing = "0.1" +tracing-subscriber = "0.3" + +[dev-dependencies] +anyhow = "1.0" +clap-verbosity-flag = {version = "2.0"} +clap = { version = "4.1", features = ["derive", "env"] } +env_logger = "0.10" +pretty_assertions = "1.3" +temp_testdir = "0.2" +test-log = "0.2" +tracing-subscriber = {version = "0.3" } diff --git a/LICENSE.txt b/LICENSE.txt new file mode 100644 index 0000000..d645695 --- /dev/null +++ b/LICENSE.txt @@ -0,0 +1,202 @@ + + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. Definitions. + + "License" shall mean the terms and conditions for use, reproduction, + and distribution as defined by Sections 1 through 9 of this document. + + "Licensor" shall mean the copyright owner or entity authorized by + the copyright owner that is granting the License. + + "Legal Entity" shall mean the union of the acting entity and all + other entities that control, are controlled by, or are under common + control with that entity. For the purposes of this definition, + "control" means (i) the power, direct or indirect, to cause the + direction or management of such entity, whether by contract or + otherwise, or (ii) ownership of fifty percent (50%) or more of the + outstanding shares, or (iii) beneficial ownership of such entity. + + "You" (or "Your") shall mean an individual or Legal Entity + exercising permissions granted by this License. + + "Source" form shall mean the preferred form for making modifications, + including but not limited to software source code, documentation + source, and configuration files. + + "Object" form shall mean any form resulting from mechanical + transformation or translation of a Source form, including but + not limited to compiled object code, generated documentation, + and conversions to other media types. + + "Work" shall mean the work of authorship, whether in Source or + Object form, made available under the License, as indicated by a + copyright notice that is included in or attached to the work + (an example is provided in the Appendix below). + + "Derivative Works" shall mean any work, whether in Source or Object + form, that is based on (or derived from) the Work and for which the + editorial revisions, annotations, elaborations, or other modifications + represent, as a whole, an original work of authorship. For the purposes + of this License, Derivative Works shall not include works that remain + separable from, or merely link (or bind by name) to the interfaces of, + the Work and Derivative Works thereof. + + "Contribution" shall mean any work of authorship, including + the original version of the Work and any modifications or additions + to that Work or Derivative Works thereof, that is intentionally + submitted to Licensor for inclusion in the Work by the copyright owner + or by an individual or Legal Entity authorized to submit on behalf of + the copyright owner. For the purposes of this definition, "submitted" + means any form of electronic, verbal, or written communication sent + to the Licensor or its representatives, including but not limited to + communication on electronic mailing lists, source code control systems, + and issue tracking systems that are managed by, or on behalf of, the + Licensor for the purpose of discussing and improving the Work, but + excluding communication that is conspicuously marked or otherwise + designated in writing by the copyright owner as "Not a Contribution." + + "Contributor" shall mean Licensor and any individual or Legal Entity + on behalf of whom a Contribution has been received by Licensor and + subsequently incorporated within the Work. + + 2. Grant of Copyright License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + copyright license to reproduce, prepare Derivative Works of, + publicly display, publicly perform, sublicense, and distribute the + Work and such Derivative Works in Source or Object form. + + 3. Grant of Patent License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + (except as stated in this section) patent license to make, have made, + use, offer to sell, sell, import, and otherwise transfer the Work, + where such license applies only to those patent claims licensable + by such Contributor that are necessarily infringed by their + Contribution(s) alone or by combination of their Contribution(s) + with the Work to which such Contribution(s) was submitted. If You + institute patent litigation against any entity (including a + cross-claim or counterclaim in a lawsuit) alleging that the Work + or a Contribution incorporated within the Work constitutes direct + or contributory patent infringement, then any patent licenses + granted to You under this License for that Work shall terminate + as of the date such litigation is filed. + + 4. Redistribution. You may reproduce and distribute copies of the + Work or Derivative Works thereof in any medium, with or without + modifications, and in Source or Object form, provided that You + meet the following conditions: + + (a) You must give any other recipients of the Work or + Derivative Works a copy of this License; and + + (b) You must cause any modified files to carry prominent notices + stating that You changed the files; and + + (c) You must retain, in the Source form of any Derivative Works + that You distribute, all copyright, patent, trademark, and + attribution notices from the Source form of the Work, + excluding those notices that do not pertain to any part of + the Derivative Works; and + + (d) If the Work includes a "NOTICE" text file as part of its + distribution, then any Derivative Works that You distribute must + include a readable copy of the attribution notices contained + within such NOTICE file, excluding those notices that do not + pertain to any part of the Derivative Works, in at least one + of the following places: within a NOTICE text file distributed + as part of the Derivative Works; within the Source form or + documentation, if provided along with the Derivative Works; or, + within a display generated by the Derivative Works, if and + wherever such third-party notices normally appear. The contents + of the NOTICE file are for informational purposes only and + do not modify the License. You may add Your own attribution + notices within Derivative Works that You distribute, alongside + or as an addendum to the NOTICE text from the Work, provided + that such additional attribution notices cannot be construed + as modifying the License. + + You may add Your own copyright statement to Your modifications and + may provide additional or different license terms and conditions + for use, reproduction, or distribution of Your modifications, or + for any such Derivative Works as a whole, provided Your use, + reproduction, and distribution of the Work otherwise complies with + the conditions stated in this License. + + 5. Submission of Contributions. Unless You explicitly state otherwise, + any Contribution intentionally submitted for inclusion in the Work + by You to the Licensor shall be under the terms and conditions of + this License, without any additional terms or conditions. + Notwithstanding the above, nothing herein shall supersede or modify + the terms of any separate license agreement you may have executed + with Licensor regarding such Contributions. + + 6. Trademarks. This License does not grant permission to use the trade + names, trademarks, service marks, or product names of the Licensor, + except as required for reasonable and customary use in describing the + origin of the Work and reproducing the content of the NOTICE file. + + 7. Disclaimer of Warranty. Unless required by applicable law or + agreed to in writing, Licensor provides the Work (and each + Contributor provides its Contributions) on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or + implied, including, without limitation, any warranties or conditions + of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A + PARTICULAR PURPOSE. You are solely responsible for determining the + appropriateness of using or redistributing the Work and assume any + risks associated with Your exercise of permissions under this License. + + 8. Limitation of Liability. In no event and under no legal theory, + whether in tort (including negligence), contract, or otherwise, + unless required by applicable law (such as deliberate and grossly + negligent acts) or agreed to in writing, shall any Contributor be + liable to You for damages, including any direct, indirect, special, + incidental, or consequential damages of any character arising as a + result of this License or out of the use or inability to use the + Work (including but not limited to damages for loss of goodwill, + work stoppage, computer failure or malfunction, or any and all + other commercial damages or losses), even if such Contributor + has been advised of the possibility of such damages. + + 9. Accepting Warranty or Additional Liability. While redistributing + the Work or Derivative Works thereof, You may choose to offer, + and charge a fee for, acceptance of support, warranty, indemnity, + or other liability obligations and/or rights consistent with this + License. However, in accepting such obligations, You may act only + on Your own behalf and on Your sole responsibility, not on behalf + of any other Contributor, and only if You agree to indemnify, + defend, and hold each Contributor harmless for any liability + incurred by, or claims asserted against, such Contributor by reason + of your accepting any such warranty or additional liability. + + END OF TERMS AND CONDITIONS + + APPENDIX: How to apply the Apache License to your work. + + To apply the Apache License to your work, attach the following + boilerplate notice, with the fields enclosed by brackets "[]" + replaced with your own identifying information. (Don't include + the brackets!) The text should be enclosed in the appropriate + comment syntax for the file format. We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright [yyyy] [name of copyright owner] + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. diff --git a/README.md b/README.md new file mode 100644 index 0000000..fef5078 --- /dev/null +++ b/README.md @@ -0,0 +1,24 @@ +[![Crates.io](https://img.shields.io/crates/d/scarus.svg)](https://crates.io/crates/scarus) +[![Crates.io](https://img.shields.io/crates/v/scarus.svg)](https://crates.io/crates/scarus) +[![Crates.io](https://img.shields.io/crates/l/scarus.svg)](https://crates.io/crates/scarus) +[![CI](https://github.com/bihealth/scarus/actions/workflows/rust.yml/badge.svg)](https://github.com/bihealth/scarus/actions/workflows/rust.yml) +[![codecov](https://codecov.io/gh/bihealth/scarus/branch/main/graph/badge.svg?token=aZchhLWdzt)](https://codecov.io/gh/bihealth/scarus) + +# SCARUS - Simple Code for ACMG Rule Utilisation and Scrutiny + +This repository contains code for the automated evaluation of ACMG criteria for sequence and structural variants. + +## Managing Project with Terraform + +``` +# export GITHUB_OWNER=bihealth +# export GITHUB_TOKEN=ghp_TOKEN + +# cd utils/terraform +# terraform init +# terraform import github_repository.scarus scarus +# terraform validate +# terraform fmt +# terraform plan +# terraform apply +``` diff --git a/codecov.yml b/codecov.yml new file mode 100644 index 0000000..b09fe13 --- /dev/null +++ b/codecov.yml @@ -0,0 +1,2 @@ +ignore: + - "examples/*" diff --git a/src/common/mod.rs b/src/common/mod.rs new file mode 100644 index 0000000..9c5ffa9 --- /dev/null +++ b/src/common/mod.rs @@ -0,0 +1,12 @@ +//! Commonly used code. + +use clap::Parser; +use clap_verbosity_flag::{InfoLevel, Verbosity}; + +/// Commonly used command line arguments. +#[derive(Parser, Debug)] +pub struct Args { + /// Verbosity of the program + #[clap(flatten)] + pub verbose: Verbosity, +} diff --git a/src/main.rs b/src/main.rs new file mode 100644 index 0000000..171dc9d --- /dev/null +++ b/src/main.rs @@ -0,0 +1,73 @@ +//! Main entry point for Scarus application. + +#![deny(clippy::pedantic)] +#![allow(clippy::must_use_candidate)] +#![allow(clippy::module_name_repetitions)] +#![warn(missing_docs)] + +use clap::{Parser, Subcommand}; + +pub mod common; +pub mod seqvars; +pub mod strucvars; + +/// CLI parser based on clap. +#[derive(Debug, Parser)] +#[command( + author, + version, + about = "scarus - ACMG rule evaluation", + long_about = "This tool provides functionality for automated ACMG rule evaluation" +)] +struct Cli { + /// Commonly used arguments + #[command(flatten)] + common: common::Args, + + /// The sub command to run + #[command(subcommand)] + command: Commands, +} + +/// Enum supporting the parsing of top-level commands. +#[allow(clippy::large_enum_variant)] +#[derive(Debug, Subcommand)] +enum Commands { + /// Structural variant related commands. + Strucvars(strucvars::Args), + /// Sequence variant related commands. + Seqvars(seqvars::Args), +} + +#[tokio::main] +async fn main() -> Result<(), anyhow::Error> { + let cli = Cli::parse(); + + // Build a tracing subscriber according to the configuration in `cli.common`. + let collector = tracing_subscriber::fmt() + .with_target(false) + .with_max_level(match cli.common.verbose.log_level() { + Some(level) => match level { + log::Level::Error => tracing::Level::ERROR, + log::Level::Warn => tracing::Level::WARN, + log::Level::Info => tracing::Level::INFO, + log::Level::Debug => tracing::Level::DEBUG, + log::Level::Trace => tracing::Level::TRACE, + }, + None => tracing::Level::INFO, + }) + .compact() + .finish(); + tracing::subscriber::set_global_default(collector)?; + + tracing::info!("Starting SCARUS -- taking a chunk out of your variants..."); + + match &cli.command { + Commands::Strucvars(args) => strucvars::run(&cli.common, args)?, + Commands::Seqvars(args) => seqvars::run(&cli.common, args)?, + } + + tracing::info!("All done. Have a nice day!"); + + Ok(()) +} diff --git a/src/seqvars/mod.rs b/src/seqvars/mod.rs new file mode 100644 index 0000000..f3f8e50 --- /dev/null +++ b/src/seqvars/mod.rs @@ -0,0 +1,25 @@ +//! ACMG rule prediction for sequence variants. + +use clap::Parser; + +/// Command line arguments for `seqvars` command. +#[derive(Parser, Debug)] +#[command(about = "ACMG rule applications for sequence variants", long_about = None)] +pub struct Args {} + +/// Main entry point for the `seqvars` command. +/// +/// # Arguments +/// +/// * `common_args` - Commonly used command line arguments. +/// * `args` - Command line arguments specific to `strucvars` command. +/// +/// # Errors +/// +/// If anything goes wrong, it returns a generic `anyhow::Error`. +pub fn run(common_args: &crate::common::Args, args: &Args) -> Result<(), anyhow::Error> { + tracing::info!(" running command `strucvars`"); + tracing::info!(" common_args = {:?}", &common_args); + tracing::info!(" args = {:?}", &args); + Ok(()) +} diff --git a/src/strucvars/mod.rs b/src/strucvars/mod.rs new file mode 100644 index 0000000..66ece16 --- /dev/null +++ b/src/strucvars/mod.rs @@ -0,0 +1,25 @@ +//! ACMG rule prediction for structural variants. + +use clap::Parser; + +/// Command line arguments for `strucvars` command. +#[derive(Parser, Debug)] +#[command(about = "ACMG rule applications for structural variants", long_about = None)] +pub struct Args {} + +/// Main entry point for the `strucvars` command. +/// +/// # Arguments +/// +/// * `common_args` - Commonly used command line arguments. +/// * `args` - Command line arguments specific to `strucvars` command. +/// +/// # Errors +/// +/// If anything goes wrong, it returns a generic `anyhow::Error`. +pub fn run(common_args: &crate::common::Args, args: &Args) -> Result<(), anyhow::Error> { + tracing::info!(" running command `strucvars`"); + tracing::info!(" common_args = {:?}", &common_args); + tracing::info!(" args = {:?}", &args); + Ok(()) +} diff --git a/utils/terraform/.gitignore b/utils/terraform/.gitignore new file mode 100644 index 0000000..5dfe310 --- /dev/null +++ b/utils/terraform/.gitignore @@ -0,0 +1,2 @@ +.terraform* +terraform.tfstate* diff --git a/utils/terraform/main.tf b/utils/terraform/main.tf new file mode 100644 index 0000000..aca322f --- /dev/null +++ b/utils/terraform/main.tf @@ -0,0 +1,16 @@ +# Mangement of the GitHub project. + +resource "github_repository" "scarus" { + name = "scarus" + description = "Automated evaluation of ACMG rules" + + visibility = "public" + + has_downloads = true + has_issues = true + has_projects = false + has_wiki = false + + allow_rebase_merge = false + allow_merge_commit = false +} diff --git a/utils/terraform/provider.tf b/utils/terraform/provider.tf new file mode 100644 index 0000000..0349641 --- /dev/null +++ b/utils/terraform/provider.tf @@ -0,0 +1 @@ +provider "github" {}