Running kGWASflow

Running kGWASflow with kgwasflow run

After the initialization step (kgwasflow init) and modifying the configuration files, kGWASflow can be run as below:

# Activating the conda environment
conda activate kgwasflow

# Change into your preferred working directory
cd path/to/your/work_dir 

# Run kgwasflow
kgwasflow run -t 16

Below are some of the run examples of kGWASflow:

Run examples:

1. Run kGWASflow with the default config file, default arguments and 16 threads:

  kgwasflow run -t 16 --snake-default

2. Run kGWASflow with a custom config file and default settings:

  kgwasflow run -t 16 -c path/to/custom_config.yaml

3. Run kGWASflow with user defined output directory:

  kgwasflow run -t 16 --output path/to/output_dir

4. Run kGWASflow in dryrun mode to see what tasks would be executed:

  kgwasflow run -t 16 -n

5. Run kGWASflow using mamba as the conda frontend:

  kgwasflow run -t 16 --conda-frontend mamba

6. Run kGWASflow and generate an HTML report:

  kgwasflow run -t 16 --generate-report

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Command Line Options

You can use --help argument to print the below help message to see all the options when using kgwasflow run:

     _     _______          __      _____  __ _               
    | |   / ____\ \        / /\    / ____|/ _| |              
    | | _| |  __ \ \  /\  / /  \  | (___ | |_| | _____      __
    | |/ / | |_ | \ \/  \/ / /\ \  \___ \|  _| |/ _ \ \ /\ / /
    |   <| |__| |  \  /\  / ____ \ ____) | | | | (_) \ V  V / 
    |_|\_\_____|   \/  \/_/    \_\_____/|_| |_|\___/ \_/\_/  
    
    kGWASflow: A Snakemake Workflow for k-mers Based GWAS
    
Usage: kgwasflow run [OPTIONS] [SNAKEMAKE_ARGS]...

  Run kGWASflow workflow.

Options:
  -s, --snakefile PATH    Path to the Snakefile.
  -c, --config-file PATH  Path to the config.yaml file
  -t, --threads INTEGER   Number of threads (default: 8).  [default: 8]
  -d, --work-dir PATH     kGWASflow working directory.
  --conda-frontend TEXT   Conda frontend to use.
  -n, --dryrun            Dry run. Do not execute the workflow, but show which
                          jobs would be executed.
  -r, --generate-report   Create a kGWASflow HTML report.
  --snake-default         Useful default snakemake arguments.
  --rerun-triggers TEXT   Rerun all jobs that have at least one of the
                          specified trigger files changed.  [default: mtime,
                          params, input, software-env, code]
  --unlock                Unlock the workflow if it is locked.
  -v, --verbose           Increase output verbosity.
  -h, --help              Show this message and exit.

  CLUSTER EXECUTION:

   kgwasflow run ... --profile [profile]

   For information on Snakemake profiles see:
   https://snakemake.readthedocs.io/en/stable/executing/cluster.html
   https://snakemake.readthedocs.io/en/stable/executing/cli.html#profiles

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Results Directory Structure

The below directory tree shows an example Results directory structure after a successful kGWASflow run.

├── logs
├── results
    ├── align_contigs
    ├── align_kmers
    ├── align_reads_with_kmers
    ├── assemble_reads_with_kmers
    ├── blast_contigs
    ├── fetch_kmers
    ├── fetch_reads_with_kmers
    ├── filter_kmers
    ├── igv_reports
    ├── kmers_count
    ├── kmers_gwas
    ├── kmers_list
    ├── kmers_table
    ├── plots
    ├── qc
    ├── reads
    └── tables

Running kGWASflow with Snakemake Commands

Information about how to use kGWASflow with Snakemake commands can be found in the Snakemake Workflow Catalog.