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Installation & Update

ashleys-qc-pipeline & mosaicatcher-pipeline dependencies

From 2.2.0, you don't need to clone both ashleys-qc-pipeline preprocessing module and mosaicatcher-pipeline. By using ashleys_pipeline_only=True combined with ashleys_pipeline=True in the configuration of MosaiCatcher, this will stop the execution after the generation of the files related to ashleys-qc-pipeline. This allow you to use a single pipeline, repository and container and limit the potential conflicts by processing the same folder (data_location) by different repositories and set of files (including the workflow/data/ref_genomes references files).

System requirements

This workflow is meant to be run in a Unix-based operating system when using the local execution profiles (tested on Ubuntu 18.04 & CentOS 7).

Minimum system requirements vary based on the use case. We highly recommend running it in a server environment with 32+GB RAM and 12+ cores.

Aside local execution, the pipeline can be run on a HPC cluster. The pipeline has been tested on SLURM-based clusters.

Installation

0. [Optional] Install Apptainer

In order to run the pipeline, you can use the Apptainer containerization tool. This will allow you to run the pipeline in a controlled environment, with all the dependencies installed and ready to use.

1. Install snakemake through conda in a dedicated env

Snakemake version compatibility

The pipeline has been tested with Snakemake version 7+. Some tests are currently ongoing to ensure compatibility with Snakemake 8+.

To install the required snakemake dependencies, you can use the following commands:

conda create -n snakemake-env \
    -c conda-forge -c bioconda snakemake==7.32.4
conda activate snakemake-env

If you prefer to use a python virtual environment, you can use the following commands:

python3 -m venv snakemake-env
source snakemake-env/bin/activate
pip install snakemake==7.32.4

Note

Instead of installing your own snakemake environment, you can load an existing snakemake module with the following command: 

module load snakemake/7.32.4-foss-2022b

2. Clone the repository and its submodules

# Clone the repository and its submodules
git clone --recurse-submodules https://github.com/friendsofstrandseq/mosaicatcher-pipeline.git && cd mosaicatcher-pipeline

# In each submodule, initialize and pull
git submodule update --init --remote --force --recursive

Pipeline update procedure

If you already use a previous version of mosaicatcher-pipeline, here is a short procedure to update it:

  • First, update all origin/ refs to latest:

git fetch --all

  • Jump to a new version & pull code:

git checkout <VERSION> && git pull

Then, to initiate or update git submodules:

git submodule update --init --remote --force --recursive