merge 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_merge_v2.28.0_cv2.cwl example_inputs.yml

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

#Using CWLTOOL
> cwltool --singularity --non-strict bedtools_merge_v2.28.0_cv2.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_merge_v2.28.0_cv2.cwl inputs.yaml > file.stdout 2> file.stderr &

Usage

```bash

toil-cwl-runner bedtools_merge_v2.28.0_cv2.cwl --help

usage: bedtools_merge_v2.28.0_cv2.cwl [-h] --input INPUT --output_file_name OUTPUT_FILE_NAME [--memory_overhead MEMORY_OVERHEAD] [--memory_per_job MEMORY_PER_JOB] [--number_of_threads NUMBER_OF_THREADS] [--distance_between_features DISTANCE_BETWEEN_FEATURES] [job_order]

positional arguments: job_order Job input json file

optional arguments: -h, --help show this help message and exit --input INPUT BEDgraph format file generated from Bedtools Genomecov module --output_file_name OUTPUT_FILE_NAME --memory_overhead MEMORY_OVERHEAD --memory_per_job MEMORY_PER_JOB --number_of_threads NUMBER_OF_THREADS --distance_between_features DISTANCE_BETWEEN_FEATURES Maximum distance between features allowed for features to be merged.