minor
Version of tools in docker image (/container/Dockerfile)
Tool
Version
Location
biometrics_minor
0.2.15
CWL
CWL specification 1.0
Use example_inputs.json to see the inputs to the cwl
Example Command using toil:
> toil-cwl-runner biometrics_minor.cwl example_inputs.json#Using CWLTOOL
> cwltool --singularity --non-strict /path/to/biometrics_minor.cwl /path/to/example_inputs.json
#Using toil-cwl-runner
> mkdir tool_toil_log
> toil-cwl-runner --singularity --logFile /path/to/tool_toil_log/cwltoil.log --jobStore /path/to/tool_jobStore --batchSystem lsf --workDir /path/to/tool_toil_log --outdir . --writeLogs /path/to/tool_toil_log --logLevel DEBUG --stats --retryCount 2 --disableCaching --maxLogFileSize 20000000000 /path/to/biometrics_minor.cwl /path/to/example_inputs.json > tool_toil.stdout 2> tool_toil.stderr &Usage
> toil-cwl-runner biometrics_minor.cwl -h
usage: biometrics_minor/0.2.15/biometrics_minor.cwl [-h] --input INPUT [--database DATABASE]
[--minor_threshold MINOR_THRESHOLD] [--prefix PREFIX]
[--plot] [--json] [--no_db_comparison]
[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.
--minor_threshold MINOR_THRESHOLD
Minor contamination threshold for bad sample.
--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.Last updated