sortbed v2.28.0_cv2

Version of tools in docker image

Tool	Version	Location
Bedtools	v2.28.0_cv2	https://github.com/arq5x/bedtools2/releases/tag/v2.28.0

CWL

• CWL specification 1.0

• Use example_inputs.yml to see the inputs to the cwl

• Example Command using toil:

toil-cwl-runner bedtools_sortbed_vcf.cwl example_input.yml

If at MSK, using the JUNO cluster you can use the following command

#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

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