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createcallregions.rst
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createcallregions.rst
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:orphan:
Create genomic call regions
===============================================
``CreateCallRegions`` · *1 contributor · 1 version*
No documentation was provided: `contribute one <https://github.com/PMCC-BioinformaticsCore/janis-bioinformatics>`_
Quickstart
-----------
.. code-block:: python
from janis_bioinformatics.tools.dawson.createcallregions.base import CreateCallRegions
wf = WorkflowBuilder("myworkflow")
wf.step(
"createcallregions_step",
CreateCallRegions(
reference=None,
regionSize=None,
)
)
wf.output("regions", source=createcallregions_step.regions)
*OR*
1. `Install Janis </tutorials/tutorial0.html>`_
2. Ensure Janis is configured to work with Docker or Singularity.
3. Ensure all reference files are available:
.. note::
More information about these inputs are available `below <#additional-configuration-inputs>`_.
4. Generate user input files for CreateCallRegions:
.. code-block:: bash
# user inputs
janis inputs CreateCallRegions > inputs.yaml
**inputs.yaml**
.. code-block:: yaml
reference: reference.fasta
regionSize: 0
5. Run CreateCallRegions with:
.. code-block:: bash
janis run [...run options] \
--inputs inputs.yaml \
CreateCallRegions
Information
------------
:ID: ``CreateCallRegions``
:URL: *No URL to the documentation was provided*
:Versions: v0.1.0
:Container: python:3.8.1
:Authors: Sebastian Hollizeck
:Citations: None
:Created: 2020-06-17
:Updated: 2020-07-16
Outputs
-----------
======= ============= ===============
name type documentation
======= ============= ===============
regions Array<String>
======= ============= ===============
Additional configuration (inputs)
---------------------------------
========== ================= ===============
name type documentation
========== ================= ===============
reference FastaFai
regionSize Integer
equalize Optional<Boolean>
========== ================= ===============