https://github.com/suzuki-shm/fastANI-in-cwl

Wrapper tool of fastANI by CWL and Docker
https://github.com/suzuki-shm/fastANI-in-cwl

bioinformatics common-workflow-language cwl genome

Last synced: 21 days ago
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Wrapper tool of fastANI by CWL and Docker

• Host: GitHub
• URL: https://github.com/suzuki-shm/fastANI-in-cwl
• Owner: suzuki-shm
• License: bsd-3-clause
• Created: 2019-03-25T02:43:45.000Z (over 5 years ago)
• Default Branch: master
• Last Pushed: 2019-05-30T02:34:20.000Z (over 5 years ago)
• Last Synced: 2024-04-17T05:52:34.479Z (7 months ago)
• Topics: bioinformatics, common-workflow-language, cwl, genome
• Language: Common Workflow Language
• Homepage:
• Size: 1.1 MB
• Stars: 1
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# fastANI in CWL

Wrapper tool of [fastANI](https://github.com/ParBLiSS/FastANI) by [CWL](https://github.com/common-workflow-language/common-workflow-language) and [Docker](https://www.docker.com)

## Dependency

* cwl-runner such as [cwltool](https://github.com/common-workflow-language/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](https://github.com/common-workflow-language/cwltool/) (`cwltool`), [`toil-cwl-runner`](https://toil.readthedocs.io/en/latest/running/cwl.html), or [`arvados-cwl-runner`](https://dev.arvados.org/projects/arvados/wiki/Running_Common_Workflow_Language_%28CWL%29_workflows_on_Arvados) 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

* [fastANI](https://www.nature.com/articles/s41467-018-07641-9)

## 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](https://github.com/ParBLiSS/FastANI/issues/22).