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generategenomefileforbedtoolscoverage.rst
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generategenomefileforbedtoolscoverage.rst
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:orphan:
Generate genome for BedtoolsCoverage
============================================================================
``GenerateGenomeFileForBedtoolsCoverage`` · *2 contributors · 1 version*
Generate --genome FILE for BedToolsCoverage
Quickstart
-----------
.. code-block:: python
from janis_bioinformatics.tools.pmac.generatebedtoolscoveragegenomefile import GenerateGenomeFileForBedtoolsCoverage
wf = WorkflowBuilder("myworkflow")
wf.step(
"generategenomefileforbedtoolscoverage_step",
GenerateGenomeFileForBedtoolsCoverage(
reference=None,
)
)
wf.output("out", source=generategenomefileforbedtoolscoverage_step.out)
*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 GenerateGenomeFileForBedtoolsCoverage:
.. code-block:: bash
# user inputs
janis inputs GenerateGenomeFileForBedtoolsCoverage > inputs.yaml
**inputs.yaml**
.. code-block:: yaml
reference: reference.fasta
5. Run GenerateGenomeFileForBedtoolsCoverage with:
.. code-block:: bash
janis run [...run options] \
--inputs inputs.yaml \
GenerateGenomeFileForBedtoolsCoverage
Information
------------
:ID: ``GenerateGenomeFileForBedtoolsCoverage``
:URL: *No URL to the documentation was provided*
:Versions: v0.1.0
:Container: python:3.8.1
:Authors: Michael Franklin, Jiaan Yu
:Citations: None
:Created: 2020-07-21 00:00:00
:Updated: 2020-06-02 00:00:00
Outputs
-----------
====== ======== ================================
name type documentation
====== ======== ================================
out TextFile Genome file for BedToolsCoverage
====== ======== ================================
Additional configuration (inputs)
---------------------------------
=============== ================ =====================
name type documentation
=============== ================ =====================
reference FastDict
output_filename Optional<String> Filename to output to
=============== ================ =====================