Update template

.cruft.json

@@ -0,0 +1,20 @@
+{
+    "template": "git@github.com:NCI-GDC/bio-python-template.git",
+    "commit": "0b6345a590be88d3cb69c007749a0e9e415ab56f",
+    "context": {
+      "cookiecutter": {
+        "full_name": "Linghao Song",
+        "email": "sxwcasd@gmail.com",
+        "github_username": "sxwcasd",
+        "project_name": "mutect2-tool",
+        "package_name": "mutect2_tool",
+        "project_short_description": "The GATK3 MuTect2 pipeline employs a "Panel of Normals" to identify additional germline mutations. This panel is generated using TCGA blood normal genomes from thousands of individuals that were curated and confidently assessed to be cancer-free. This method allows for a higher level of confidence to be assigned to somatic variants that were called by the MuTect2 pipeline.",
+        "min_python_version": "3.9",
+        "github_repo": "https://github.com/NCI-GDC/mutect2-tool",
+        "commit": "0b6345a590be88d3cb69c007749a0e9e415ab56f",
+        "_template": "git@github.com:NCI-GDC/bio-python-template.git"
+      }
+    },
+    "directory": null,
+    "checkout": null
+  }

.dockerignore

@@ -0,0 +1,110 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+_version.py
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# direnv
+.envrc
+.direnv/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# VSCode
+.vscode/
+test-reports/

.gitignore

@@ -107,3 +107,11 @@ ENV/
 
 # VSCode
 .vscode/
+test-reports/
+
+# Gitlab CI - automatically created, break flit validation
+vars.env
+gl-code-quality-report.html
+
+# Added in base-container builder image
+aws-lc

.gitlab-ci.yml

@@ -0,0 +1,11 @@
+---
+include:
+  - project: nci-gdc/gitlab-templates
+    ref: master
+    file:
+      - templates/global/full.yaml
+      - templates/python/full.yaml
+
+variables:
+  BUILD_PY_VERSION: python3.9
+  RELEASE_PY_VERSION: python3.9

.pre-commit-config.yaml

@@ -1,31 +1,33 @@
 default_stages: [commit, push]
 default_language_version:
-  python_venv: python3.6
+  python_venv: python3.9
 
 repos:
-  - repo: git@github.com:Yelp/detect-secrets
-    rev: v0.13.1
+  - repo: https://github.com/Yelp/detect-secrets
+    rev: v1.5.0
     hooks:
       - id: detect-secrets
         args: ['--baseline', '.secrets.baseline']
+        exclude: ^(\.cruft\.json)$
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v2.4.0
+    rev: v5.0.0
     hooks:
       - id: check-yaml
       - id: check-toml
       - id: check-json
       - id: detect-aws-credentials
         args: ["--allow-missing-credentials"]
       - id: detect-private-key
-  - repo: https://github.com/asottile/seed-isort-config
-    rev: v1.9.3
+      - id: end-of-file-fixer
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: 'v0.9.9'
     hooks:
-      - id: seed-isort-config
-  - repo: https://github.com/pre-commit/mirrors-isort
-    rev: v4.3.21
+      - id: ruff
+        args: [ '--select', 'I', '--fix' ]
+      - id: ruff-format
+  - repo: https://github.com/cruft/cruft
+    rev: 2.16.0
     hooks:
-      - id: isort
-  - repo: https://github.com/psf/black
-    rev: 19.10b0
-    hooks:
-      - id: black
+      - id: cruft
+        name: cruft
+        entry: bash -c 'cruft check || true' --

.secrets.baseline

@@ -1,9 +1,9 @@
 {
   "exclude": {
-    "files": null,
+    "files": "^.secrets.baseline$",
     "lines": null
   },
-  "generated_at": "2020-07-23T15:24:59Z",
+  "generated_at": "2020-07-21T15:11:38Z",
   "plugins_used": [
     {
       "name": "AWSKeyDetector"

Dockerfile

@@ -1,27 +1,36 @@
+ARG REGISTRY=docker.osdc.io/ncigdc
+ARG BASE_CONTAINER_VERSION=latest
+
 FROM quay.io/ncigdc/gatk:3.7 AS gatk
-FROM quay.io/ncigdc/python37 AS python
-FROM quay.io/ncigdc/bio-openjdk:8u282-slim
+FROM ${REGISTRY}/python3.9-builder:${BASE_CONTAINER_VERSION} as builder
+ENV TINI_VERSION v0.19.0
+ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini /tini
+RUN chmod +x /tini
 
-ENV BINARY mutect2-tool
-LABEL maintainer="sli6@uchicago.edu"
-LABEL version="nightly-2016-02-25-gf39d340"
-LABEL description="GATK3 nightly-2016-02-25-gf39d340"
+COPY ./ /mutect2_tool
 
-COPY --from=python / /
-COPY --from=gatk /usr/local/bin/ /usr/local/bin/
+WORKDIR /mutect2_tool
 
-COPY ./dist/ /opt
-WORKDIR /opt
+RUN pip install tox && tox -e build
 
-RUN apt-get update \
-	&& apt-get install make \
-	&& rm -rf /var/lib/apt/lists/*
+FROM ${REGISTRY}/python3.9:${BASE_CONTAINER_VERSION}
 
-RUN make init-pip \
-  && ln -s /opt/bin/${BINARY} /usr/local/bin/${BINARY}
+LABEL org.opencontainers.image.title="mutect2_tool" \
+      org.opencontainers.image.description="The GATK3 MuTect2 pipeline employs a 'Panel of Normals' to identify additional germline mutations. This panel is generated using TCGA blood normal genomes from thousands of individuals that were curated and confidently assessed to be cancer-free. This method allows for a higher level of confidence to be assigned to somatic variants that were called by the MuTect2 pipeline." \
+      org.opencontainers.image.source="https://github.com/NCI-GDC/mutect2-tool" \
+      org.opencontainers.image.vendor="NCI GDC"
+
+COPY --from=builder /mutect2_tool/dist/*.whl /mutect2_tool/
+COPY requirements.txt /mutect2_tool/
+
+WORKDIR /mutect2_tool
+
+RUN pip install --no-deps -r requirements.txt \
+	&& pip install --no-deps *.whl \
+	&& rm -f *.whl requirements.txt
+
+USER app
 
-ENV TINI_VERSION v0.19.0
-ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini /tini
-RUN chmod +x /tini
 ENTRYPOINT ["/tini", "--", "mutect2_tool"]
+
 CMD ["--help"]

LICENSE

@@ -1,4 +1,4 @@
-Apache License
+                                 Apache License
                            Version 2.0, January 2004
                         http://www.apache.org/licenses/
 
@@ -178,15 +178,15 @@ Apache License
    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 "{}"
+      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}
+   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.