Init with a dummy C++ code + associated Snakefile, with a bundled action

* Initial plan

* Add C++ hello world with Snakemake workflow and conda environment

Co-authored-by: imallona <8280371+imallona@users.noreply.github.com>

* Fix Snakefile build logic and update README with usage documentation

Co-authored-by: imallona <8280371+imallona@users.noreply.github.com>

* Add GitHub Actions workflow for Snakemake execution

Co-authored-by: imallona <8280371+imallona@users.noreply.github.com>

* Add explicit permissions to GitHub workflow for security

Co-authored-by: imallona <8280371+imallona@users.noreply.github.com>

* Remove CodeQL build artifacts and update .gitignore

Co-authored-by: imallona <8280371+imallona@users.noreply.github.com>

* Fix paths

* Fix CI/CD workflow to use Mambaforge for mamba availability

Co-authored-by: imallona <8280371+imallona@users.noreply.github.com>

* Use Miniforge3 instead of deprecated Mambaforge and explicitly install mamba

Co-authored-by: imallona <8280371+imallona@users.noreply.github.com>

* Remove verification

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: imallona <8280371+imallona@users.noreply.github.com>
Co-authored-by: Izaskun Mallona <izaskun.mallona@gmail.com>

Author: Copilot

.github/workflows/snakemake.yml

@@ -0,0 +1,60 @@
+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

@@ -0,0 +1,5 @@
+build/
+output/
+.snakemake/
+_codeql_detected_source_root
+src/_codeql_build_dir/

README.md

@@ -1,2 +1,39 @@
 # 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

@@ -0,0 +1,7 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - cmake>=4.1
+  - cxx-compiler

src/CMakeLists.txt

@@ -0,0 +1,8 @@
+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

@@ -0,0 +1,6 @@
+#include <iostream>
+
+int main() {
+    std::cout << "Hello World!" << std::endl;
+    return 0;
+}

workflow/Snakefile

@@ -0,0 +1,38 @@
+#!/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

@@ -0,0 +1 @@
+../src/