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Seprate BAMs v1.8.1

Version of tools in docker image (../marianas_process_loop_umi_1.8.1/container/Dockerfile)

Tool Version Location
java base image 8 -
Marianas 1.8.1 https://github.com/juberpatel/Marianas/releases/download/v1.8.1/Marianas-1.8.1.jar

CWL

  • CWL specification 1.0
  • Use example_inputs.yaml to see the inputs to the cwl
  • Example Command using toil:
    > toil-cwl-runner marianas_seprate_bams_1.8.1.cwl example_inputs.yaml

Usage

usage: marianas_separate_bams_1.8.1/marianas_separate_bams_1.8.1.cwl
       [-h] --input_bam INPUT_BAM [job_order]

positional arguments:
  job_order             Job input json file

optional arguments:
  -h, --help            show this help message and exit
  --input_bam INPUT_BAM