How to run QuaC pipeline
After proper installation and configuration, QuaC pipeline can be run using the
wrapper/CLI (command line interface) tool src/run_quac.py
.
Command line interface
$ python src/run_quac.py -h
usage: run_quac.py [-h] --sample_config SAMPLE_CONFIG --pedigree PEDIGREE
--quac_watch_config QUAC_WATCH_CONFIG [--workflow_config]
[--snakemake_cluster_config] [--outdir] [--tmp_dir]
[--exome] [--include_prior_qc] [--allow_sample_renaming]
[-e] [-n] [--cli_cluster_config] [--log_dir]
Command line interface to QuaC pipeline.
optional arguments:
-h, --help show this help message and exit
QuaC snakemake workflow options:
--sample_config SAMPLE_CONFIG
Sample config file in TSV format. Provides sample name
and necessary input filepaths (bam, vcf, etc.).
Required. (default: None)
--pedigree PEDIGREE Pedigree filepath. Must correspond to samples
mentioned in configfile via --sample_config. Required.
(default: None)
--quac_watch_config QUAC_WATCH_CONFIG
YAML config path specifying QC thresholds for QuaC-
Watch. See directory 'configs/quac_watch/' in quac
repo for the included config files. Required.
(default: None)
--workflow_config YAML config path specifying filepath to dependencies
of QC tools used in snakemake workflow (default:
configs/workflow.yaml)
--snakemake_cluster_config
Cluster config json file. Needed for snakemake to run
jobs in cluster. Edit template file
'configs/snakemake_cluster_config.json' to suit your
SLURM environment. (default: None)
--outdir Out directory path (default:
data/quac/results/test_project/analysis)
--tmp_dir Directory path to store temporary files created by the
workflow (default: data/quac/tmp)
--exome Flag to run the workflow in exome mode. WARNING:
Please provide appropriate configs via
--quac_watch_config. (default: False)
--include_prior_qc Flag to additionally use prior QC data as input. See
documentation for more info. (default: False)
--allow_sample_renaming
Flag to allow sample renaming in MultiQC report. See
documentation for more info. (default: False)
-e , --extra_args Pass additional custom args to snakemake. Equal symbol
is needed for assignment as in this example: -e='--
forceall' (default: None)
-n, --dryrun Flag to dry-run snakemake. Does not execute anything,
and just display what would be done. Equivalent to '--
extra_args "-n"' (default: False)
QuaC wrapper options:
--cli_cluster_config
Cluster config json file to run parent workflow job in
cluster. Edit template file
'configs/cli_cluster_config.json' to suit your SLURM
environment. (default: None)
--log_dir Directory path where logs (both workflow's and
wrapper's) will be stored (default: data/quac/logs)
Example usage
Refer to commands used in system testing for example usage.