v1.0.0

Version of tools in docker image (/container/Dockerfile)

Dockerfile uses biocontainers/biocontainers:latest as a base image and installs tools from bioconda.

Tool	Version	Location	Notes
biocontainers	latest	https://hub.docker.com/r/biocontainers/biocontainers/	base image; "latest" not actually latest version, just tag name on docker hub
bamtools	2.4.0	https://bioconda.github.io/recipes/bamtools/README.html	-
ngs-disambiguate	2016.11.10	https://bioconda.github.io/recipes/ngs-disambiguate/README.html	-

CWL

• CWL specification 1.0

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

• Example Command using toil:

    > toil-cwl-runner disambiguate_1.0.0.cwl example_inputs.yaml

Command

USAGE:

   cwltool disambiguate_1.0.0.cwl \
      --prefix <string> \
      --output_dir <string> \
      [--aligner <string>] \
      <species_a_bam> <species_b_bam>

Where:

   --prefix <string>
     (required)  Sample ID or name used as prefix. Do not include .bam

   --output_dir <string>
     (required)  Output directory

   --aligner <string>
     Aligner option {bwa(default),tophat,hisat2,star}

   <species_a_bam>
     (required)  Species A BAM file

   <species_b_bam>
     (required)  Species B BAM file