Redmar-van-den-Berg/snakemake-module-example

Example of combining multiple Snakemake files as modules

snakemake-module-example

Example of a snakemake project using snakemake modules.

Explanation

This project consists of three different Snakefiles, two of which are used as modules by the third. Each of the Snakefiles are fully fledged pipelines, that can be executed independenly as well as be used as modules.

qc-seq

Firstly, there is the qc-seq Snakefile, which runs cutadapt on two input fastq files. You can run this Snakemake pipeline directly with

snakemake  -j1 --use-singularity --config forward=tests/data/micro_rg1_R1.fq.gz reverse=tests/data/micro_rg1_R1.fq.gz -s modules/qc-seq/Snakefile

This will produce two trimmed fastq files in your working directory, trimmed_R1.fastq.gz and trimmed_R2.fastq.gz.

alignment

The second Snakefile has a workflow to map reads to the reference, producing a bam file. This pipeline can be run directly with

snakemake -j1 --use-singularity --config forward=tests/data/micro_rg1_R1.fq.gz reverse=tests/data/micro_rg1_R1.fq.gz reference=tests/data/reference/ref.fa -s modules/align/Snakefile

This produces the file alignment.sorted.bam in the current working directory.

The main pipeline

The main pipeline does not have any rules of it's own, but combines the rules from the qc-seq and alignment modules together to produce its output files. You can run the main pipeline with

snakemake -j1 --use-singularity --config forward=tests/data/micro_rg1_R1.fq.gz reverse=tests/data/micro_rg1_R1.fq.gz reference=tests/data/reference/ref.fa -s Snakefile

This will produce the file from-main.bam in the current working directory. Please see the Snakefile in the top level folder to see how the two modules are connected together.

Installation

Download the repository from github

git clone https://github.com/Redmar-van-den-Berg/snakemake-module-example.git

Install and activate the conda environment.

conda env create --file environment.yml
conda activate snakemake-module-example

Settings

There are three levels where configuration options are set, in decreasing order of priority.

1. Flags passed to snakemake using --config, or in the specified --configfile.
2. Setting specified in the PEP project configuration, under the key snakemake-module-example
3. The default settings for the pipeline, as specified in the common.smk file

Tests

You can run the tests that accompany this pipeline with the following commands

# Check if requirements are installed, and run linting on the Snakefile
pytest --kwd --tag sanity

# Test the pipeline settings in dry-run mode
pytest --kwd --tag dry-run

# Test the performance of the pipeline by running on the test data
pytest --kwd --tag integration