These pipelines facilitate the running of the Cactus whole genome alignment tool efficiently on SLURM (and possibly other) clusters.

Tutorials available on the FAS Informatics website:

<Whole genome alignment with Progressive Cactus>

<Adding a genome to a whole genome alignment>

<Adding an outgroup to a whole genome alignment>

<Replacing a genome in a whole genome alignment>

<Pangenome inference with Minigraph-Cactus>

Installation

Installation is done simply by cloning the repository:

git clone https://github.com/harvardinformatics/cactus-snakemake.git

However, Snakemake and Singularity are required as dependencies. For more information, see the setup instructions in any of the tutorials linked above.

Usage

Each pipeline has a different config file that is required to specify input and output options and cluster resources.

With the config file setup, the pipelines are generally run as:

snakemake -j <number of jobs to submit simultaneously> -e slurm -s </path/to/snakefile.smk> --configfile </path/to/your/snakmake-config.yml>

💡 Tip: Cannon cluster Snakemake plugin

If you are on the Harvard Cannon cluster, you can use the snakemake-executor-plugin-cannon to do automatic partition selection instead of the generic SLURM executor plugin. Install the plugin with pip or mamba and then use -e cannon in all of your commands instead of -e slurm.

For more information, see the setup and run instructions in each of the tutorials linked above.

Meta config options

Several meta config options exist across pipelines as pseudo-command line flags

Command line flag	Description
--config display=T	Print the current config settings and exit
--config info=T	Display some information about the pipelines, including version and last commit date
--config version=T	Display the version of the pipeline
--config prep=T	Run all pre-processing steps and exit (e.g. output directory creation, cactus image download, running cactus-prepare).
--config debug=T	The same as prep, but display extra information about the pre-processing steps.