The python package source code and Docker file are located on GitHub.
> toil-cwl-runner biometrics_genotype.cwl example_inputs.yaml
usage: biometrics_genotype.cwl [-h] --input INPUT [--database DATABASE]
[--discordance_threshold DISCORDANCE_THRESHOLD]
[--prefix PREFIX] [--plot] [--json]
[--no_db_comparison] [--threads THREADS]
[job_order]
positional arguments:
job_order Job input json file
optional arguments:
-h, --help show this help message and exit
--input INPUT Can be one of three types: (1) path to a CSV file
containing sample information (one per line). For
example: sample_name,sample_bam,sample_type,sample_sex
,sample_group. (2) Path to a '*.pk' file that was
produced by the 'extract' tool. (3) Name of the sample
to analyze; this assumes there is a file named
'{sample_name}.pk' in your database directory. Can be
specified more than once.
--database DATABASE Directory to store the intermediate files after
running the extraction step.
--discordance_threshold DISCORDANCE_THRESHOLD
Discordance values less than this are regarded as
matching samples. (default: 0.05)
--prefix PREFIX Output file prefix.
--plot Also output plots of the data.
--json Also output data in JSON format.
--no_db_comparison Do not compare the sample(s) you provided to all
samples in the database, only compare them with each
other.
--threads THREADS Number of threads to use.
