genomake CLI

genomake

genomake [-h] {chromake,...} ...

Command-line interface for genomake, a python package to analyze genomic sequencing data.

Commands

Command Description
chromake Run the chromake pipeline to align ChIP-seq and ATAC-seq data and identify enriched peaks.
(future) Additional pipelines will be added in future releases.

Global options

Name Type Description
-h, --help flag Show help message and exit.

genomake chromake

genomake chromake \
  --config-path CONFIG_PATH \
  [--jobs JOBS] \
  [--cores CORES] \
  [--local-cores LOCAL_CORES] \
  [--others-snakemake OTHERS_SNAKEMAKE] \
  [--print-only]

Run the chromake pipeline to align ChIP-seq and ATAC-seq data and identify enriched peaks.
This command wraps a Snakemake workflow and exposes common resource-management options.

Parameters

Name Type Description Default
--config-path, -c str Path to the YAML configuration file describing samples, references, and pipeline parameters. See genomake.pipelines.chromake.scripts.config.create_example_config() for an example. required
--jobs, -j int Maximum number of Snakemake jobs to run concurrently. 5
--cores int Maximum number of CPU cores used in parallel (Snakemake --cores). 150
--local-cores int In cluster/cloud mode, use at most N cores of the host machine in parallel (default: number of CPU cores of the host). The cores are used to execute local rules. This option is ignored when not in cluster/cloud mode. (Snakemake --local-cores). 1
--others-snakemake str Additional arguments passed verbatim to Snakemake (e.g. executor, SLURM options). ""
--print-only, -p flag Print the generated Snakemake command and exit without executing the workflow. False

Examples

Run the pipeline locally:

genomake chromake -c config.yaml

Run on a SLURM cluster:

genomake chromake \
  -c config.yaml \
  --jobs 8 \
  --cores 250 \
  --others-snakemake "--executor slurm --default-resources slurm_account=singlecell"

Print the Snakemake command without running it:

genomake chromake -c config.yaml --print-only