Add Docker image build infrastructure

Set up repository for building and publishing a read QC tools Docker image:
- Dockerfile based on micromamba with conda environment
- GitHub Actions workflow for multi-arch builds (amd64/arm64)
- Automatic publishing to ghcr.io on branch/tag push

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Author: dpark01

.dockerignore

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+# Git
+.git/
+.gitignore
+
+# GitHub
+.github/
+
+# Documentation
+README.md
+
+# Scripts (not needed in image)
+scripts/
+
+# IDE
+.idea/
+.vscode/
+
+# OS
+.DS_Store
+
+# Local testing
+*.log
+tmp/

.github/workflows/docker.yml

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+name: Build and Push Docker Image
+
+on:
+  push:
+    branches:
+      - '**'
+    tags:
+      - '**'
+  pull_request:
+    branches:
+      - main
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Log in to Container Registry
+        if: github.event_name != 'pull_request'
+        uses: docker/login-action@v3
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels)
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+          tags: |
+            # For branches: use branch name
+            type=ref,event=branch
+            # For tags: use tag name
+            type=ref,event=tag
+            # For PRs: use pr-<number>
+            type=ref,event=pr
+            # Add 'latest' tag for default branch
+            type=raw,value=latest,enable={{is_default_branch}}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          platforms: linux/amd64,linux/arm64
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max

.gitignore

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+# Python
+__pycache__/
+*.py[cod]
+*.egg-info/
+.eggs/
+dist/
+build/
+
+# IDE
+.idea/
+.vscode/
+*.swp
+*.swo
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Local testing
+*.log
+tmp/

Dockerfile

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+FROM mambaorg/micromamba:2.4.0-ubuntu24.04
+
+# Copy environment file and install dependencies
+COPY --chown=$MAMBA_USER:$MAMBA_USER env.yaml /tmp/env.yaml
+RUN micromamba install -y -n base -f /tmp/env.yaml && \
+    micromamba clean --all --yes
+
+# Enable conda environment activation for subsequent RUN commands
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
+
+# Verify key tools are available
+RUN python --version && \
+    samtools --version | head -1 && \
+    fastqc --version && \
+    multiqc --version
+
+# Set working directory
+WORKDIR /data

README.md

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+# read-qc-tools
+
+Docker image containing tools for read QC and processing.
+
+## Included Tools
+
+- **fastqc** - Quality control for high throughput sequence data
+- **multiqc** - Aggregate results from bioinformatics analyses
+- **samtools** - Tools for manipulating SAM/BAM files
+- **python 3.12** with biopython and pysam
+- **GNU parallel** - Shell tool for executing jobs in parallel
+- **jq** - Command-line JSON processor
+- **pigz** - Parallel gzip
+- **zstd** - Zstandard compression
+
+## Usage
+
+### Pull from GitHub Container Registry
+
+```bash
+docker pull ghcr.io/OWNER/read-qc-tools:main
+```
+
+Replace `OWNER` with the GitHub organization or username.
+
+### Run interactively
+
+```bash
+docker run --rm -it -v $(pwd):/data ghcr.io/OWNER/read-qc-tools:main bash
+```
+
+### Run a specific command
+
+```bash
+docker run --rm -v $(pwd):/data ghcr.io/OWNER/read-qc-tools:main fastqc reads.fastq.gz
+```
+
+## Building Locally
+
+```bash
+./scripts/build.sh
+```
+
+Or with custom image name/tag:
+
+```bash
+IMAGE_NAME=my-image TAG=dev ./scripts/build.sh
+```
+
+## Multi-Architecture Support
+
+The image is built for both `linux/amd64` (Intel/AMD) and `linux/arm64` (Apple Silicon, ARM servers). Docker will automatically pull the correct architecture for your platform.
+
+## Modifying the Environment
+
+Edit `env.yaml` to add or remove conda packages, then rebuild.

env.yaml

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+name: base
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  # QC tools
+  - fastqc
+  - multiqc
+
+  # Alignment/BAM tools
+  - samtools
+
+  # Python and libraries
+  - python=3.12
+  - biopython
+  - pysam
+
+  # CLI utilities
+  - parallel  # GNU parallel
+  - jq
+  - pigz
+  - zstd

scripts/build.sh

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+#!/usr/bin/env bash
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+REPO_ROOT="$(dirname "$SCRIPT_DIR")"
+
+# Default image name
+IMAGE_NAME="${IMAGE_NAME:-read-qc-tools}"
+TAG="${TAG:-local}"
+
+cd "$REPO_ROOT"
+
+echo "Building Docker image: ${IMAGE_NAME}:${TAG}"
+
+docker build \
+    -t "${IMAGE_NAME}:${TAG}" \
+    .
+
+echo "Build complete: ${IMAGE_NAME}:${TAG}"
+echo ""
+echo "Run with: docker run --rm -it -v \$(pwd):/data ${IMAGE_NAME}:${TAG}"