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fastANI in CWL

Wrapper tool of fastANI by CWL and Docker

Dependency

  • cwl-runner such as cwltool
  • Docker
    • If you cannot use docker, this tool runs with --no-container options.
    • However, you have to install dependent tools of fastANI, such as Autoconf, GSL|Boost, Zlib, and C++ compiler

How to use

With the CWL reference implementation (cwltool), toil-cwl-runner, or arvados-cwl-runner as your cwl-runner:

cwl-runner --outdir ${PATH_TO_OUTPUT_DIR} \
           fastANI.cwl \
           --ref ${PATH_TO_REF_SEQUENCE_FILE} \
           --query  ${PATH_TO_QUERY_SEQUENCE_FILE}

For other runners an input object is required:

inputs.yml

ref:
  class: File
  path: path/to/ref/file
query:
  class: File
  path: path/to/query/file

cwl-runner --outdir ${PATH_TO_OUTPUT_DIR} \
           fastANI.cwl \
           inputs.yml

References

FAQ

My output is empty

Are the length of the sequence being used and the similarity to the realistic genome sequence sufficient? For speeding up, fastANI tunes the k-mer sequence used for the hash table to the one used for the coding sequence. Therefore, the result become empty if such a gene region is not included in the input sequence. For more details, see this issue.