simplex_filter v0.1.8

Version of tools in docker image

Tool	Version	Location
fgbio_postprocessing	0.1.8	https://github.com/msk-access/fgbio_postprocessing

CWL

• CWL specification 1.0

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

• Example Command using toil:

    > toil-cwl-runner fgbio_postprocessing_simplex_filter_0.1.8.cwl example_inputs.yaml

Usage

usage: fgbio_postprocessing_simplex_filter_0.1.8/fgbio_postprocessing_simplex_filter_0.1.8.cwl
       [-h] [--memory_per_job MEMORY_PER_JOB]
       [--memory_overhead MEMORY_OVERHEAD]
       [--number_of_threads NUMBER_OF_THREADS] --input_bam INPUT_BAM
       [--output_file_name OUTPUT_FILE_NAME]
       [job_order]

positional arguments:
  job_order             Job input json file

optional arguments:
  -h, --help            show this help message and exit
  --memory_per_job MEMORY_PER_JOB
                        Memory per job in megabytes
  --memory_overhead MEMORY_OVERHEAD
                        Memory overhead per job in megabytes
  --number_of_threads NUMBER_OF_THREADS
  --input_bam INPUT_BAM
                        Input file (bam or sam). Required.
  --output_file_name OUTPUT_FILE_NAME
                        Output file (bam or sam).