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🚀 Quick Start

Get up and running with MosaiCatcher in minutes.

Note

  • Ensure Snakemake is installed (see Installation)
  • Snakemake can be loaded via module system, conda, or Pixi
  • For containerized execution, Apptainer is used (replaces Singularity)

Install Snakemake (if needed)

pixi install snakemake
pixi run snakemake --version

Option 2: Using conda

conda install -c conda-forge -c bioconda snakemake==9

Option 3: Using module system (EMBL)

module avail snakemake
module load snakemake/<version>
snakemake --version

Activate Snakemake environment

Before running, ensure Snakemake is available:

which snakemake

Run on example data

Test the pipeline with included example data:

snakemake \
    --cores 6 \
    --configfile .tests/config/simple_config_mosaicatcher.yaml \
    --sdm conda

For containerized execution (requires Apptainer):

snakemake \
    --cores 6 \
    --configfile .tests/config/simple_config_mosaicatcher.yaml \
    --sdm conda apptainer \
    --apptainer-args "-B /<disk>:/<disk>"

The container image (ghcr.io/friendsofstrandseq/mosaicatcher-pipeline:hg38-v2.4.0 for hg38) is pulled automatically on first run.

Run on your own data

Analyze your own Strand-Seq samples:

snakemake \
    --cores <N> \
    --config data_location=<PATH> \
    --sdm conda

Replace: - <N> with number of cores to use - <PATH> with path to your data folder

Generate report (optional)

Create an interactive HTML report:

snakemake \
    --cores <N> \
    --config data_location=<PATH> \
    --report <report>.zip \
    --report-stylesheet workflow/report/custom-stylesheet.css

Next: See Input Data Formats to prepare your data correctly.