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snakebuild

A lightweight generator for Snakemake workflows

snakebuild is a command-line tool that automatically generates a complete, ready-to-run Snakemake workflow directory.
It supports both local (core) workflows and lightweight cloud mode, with automatic generation of configuration files and step lists.

Features

  • Generate a fully structured Snakemake Snakefile
  • Automatically create config.yaml if none is provided
    • Includes placeholder paths
    • Warns user to update input files
  • Supports @file syntax to load step lists: 
    snakebuild --steps @steps.txt
  • Supports cloud and core modes:
    • Core mode uses a config.yaml (auto-generated if needed)
    • Cloud mode does not require a config file
  • Automatically creates the output directory
  • Compatible with dynamic rule sets (core vs cloud rules)
  • Clean CLI with clear error messages

Installation

pip install snakebuilder

Or from source:

git clone https://github.com/<your-org>/snakebuilder.git
cd snakebuilder
pip install -e .

Usage

Basic usage (auto-generates config.yaml):

snakebuild --steps processing detect --outdir ./myrun

This creates:

myrun/
    Snakefile
    config.yaml   (placeholder version)

Using a config file

snakebuild --config config.yaml --steps processing detect --outdir run1

The config file is copied into the output directory, ensuring reproducibility.

Using @file syntax for steps

Create a file:

steps.txt

# Preprocessing
 decompress_inputs 
 fastp 
 build_bowtie2_index 
 remove_rrna 
 build_star_index 
 star_align 
 prep_circtools 

 #run detection
 detect

Then run:

snakebuild --steps @steps.txt --outdir run_pipeline

You can mix syntax:

snakebuild --steps detect @extra_steps.txt circtest

Cloud mode

Cloud mode ignores the local config and relies on cloud-based settings:

snakebuild --cloud --steps detect circtest

This is built for circtools.cloud wont work on CLI

⚠ Placeholder Config

If no config is provided, snakebuild generates a default config.yaml with clear placeholder values:

⚠  No config provided. Generating placeholder config.yaml.
   Make sure to replace the placeholder paths with your actual files!

This ensures the workflow remains self-contained while reminding the user to edit paths.

Example: Full Pipeline

snakebuild     --steps @full_pipeline.txt     --outdir workflow_run --species mm

Where full_pipeline.txt contains:

check_inputs
fastp
build_bowtie2_index
remove_rrna
build_star_index
star_align
prep_circtools
detect

This will generate a circtools processing and detection pipeline for a given species using a generated config file that references genomes in BioDB.

snakemake --rerun-incomplete --snakefile ./Snakefile  --configfile ./config.yaml --cores 16 -p
'''


This will generate a snakefile that cam be used to process genomic data and detect circular RNAs!

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