toil-cwl-runner bedtools_sortbed_vcf.cwl example_input.yml
#Using CWLTOOL
cwltool --singularity --non-strict bedtools_sortbed_vcf.cwl inputs.yaml
#Using toil-cwl-runner
mkdir run_directory
toil-cwl-runner --singularity --logFile path/to/run_directory/cwltoil.log --jobStore path/to/jobStore --batchSystem lsf --workDir /path/to/run_directory --outdir /path/to/run_directory --writeLogs /path/to/run_directory --logLevel DEBUG --stats --retryCount 2 --disableCaching --maxLogFileSize 20000000000 bedtools_sortbed_vcf.cwl inputs.yaml > file.stdout 2> file.stderr &
Usage: bedtools_sortbed_vcf.cwl [-h] --input INPUT [job_order]
positional arguments:
job_order Job input json file
optional arguments:
-h, --help show this help message and exit
--input INPUT input VCF file
