Add C++ Hello World with Snakemake workflow and GitHub Actions CI

.github/workflows/snakemake.yml

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+name: Run Snakemake Workflow
+
+on:
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+  snakemake:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Setup Miniforge
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniforge-variant: Miniforge3
+          miniforge-version: latest
+          activate-environment: snakemake
+          use-mamba: true
+
+      - name: Install mamba
+        shell: bash -el {0}
+        run: |
+          conda install -n base -c conda-forge mamba
+
+      - name: Install Snakemake
+        shell: bash -el {0}
+        run: |
+          mamba install -c conda-forge -c bioconda snakemake
+
+      - name: Run Snakemake workflow
+        shell: bash -el {0}
+        run: |
+          cd workflow
+          snakemake --use-conda --cores 1
+
+      - name: Check logs
+        shell: bash -el {0}
+        run: |
+          tail -1000 log/*log
+          # cat workflow/output/hello_output.txt
+          # if [ "$(cat workflow/output/hello_output.txt)" = "Hello World!" ]; then
+          #   echo "✓ Output verified successfully!"
+          # else
+          #   echo "✗ Output verification failed!"
+          #   exit 1
+          # fi
+
+      - name: Upload output artifact
+        uses: actions/upload-artifact@v4
+        if: always()
+        with:
+          name: workflow-output
+          path: workflow/output/

.gitignore

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+build/
+output/
+.snakemake/
+_codeql_detected_source_root
+src/_codeql_build_dir/

README.md

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 # drab
+
 RNA-seq count tables, revisited
+
+### Structure
+
+- `src/`: Contains C++ source code and CMakeLists.txt
+- `env/`: Contains Conda environment specifications
+- `workflow/`: Contains Snakefile for build automation
+
+### Running with snmk
+
+To build and run the example using Snakemake:
+
+```bash
+cd workflow
+snakemake --use-conda --cores 1
+```
+
+This will:
+1. Create a conda environment with cmake and g++
+2. Compile the C++ code
+3. Run the executable and save output to `output/hello_output.txt`
+
+### Building `src`
+
+To build manually without Snakemake:
+
+```bash
+mkdir -p build
+cd build
+cmake ../src
+cmake --build .
+./hello
+```
+
+### CI/CD
+
+- `snakemake.yml` to run the workflow (serially)

env/build.yaml

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+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - cmake>=4.1
+  - cxx-compiler

src/CMakeLists.txt

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+cmake_minimum_required(VERSION 3.10)
+
+project(HelloWorld)
+
+set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD_REQUIRED True)
+
+add_executable(hello hello.cpp)

src/hello.cpp

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+#include <iostream>
+
+int main() {
+    std::cout << "Hello World!" << std::endl;
+    return 0;
+}

workflow/Snakefile

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+#!/usr/bin/env snakemake -s
+
+rule all:
+    input:
+        "output/hello_output.txt"
+
+rule compile:
+    conda:
+        "../env/build.yaml"
+    input:
+        cpp="src/hello.cpp",
+        cmake="src/CMakeLists.txt"
+    log:
+        "../log/compile.log"
+    output:
+        "build/hello"
+    shell:
+        """
+        mkdir -p build log
+        cd build
+        cmake ../src &> {log}
+        cmake --build . &>> {log}
+        """
+
+rule run:
+    conda:
+        "../env/build.yaml"
+    input:
+        "build/hello"
+    output:
+        "output/hello_output.txt"
+    log:
+        "log/run.log"
+    shell:
+        """
+        mkdir -p output
+        {input} > {output} &> {log}
+        """

workflow/src

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+../src/