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generateintervalsbychromosome.rst
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generateintervalsbychromosome.rst
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:orphan:
Generating genomic intervals by chromosome
==========================================================================
``GenerateIntervalsByChromosome`` · *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.pmac.generatintervalsbychromosome.generateintervalsbychromosome import GenerateIntervalsByChromosome
wf = WorkflowBuilder("myworkflow")
wf.step(
"generateintervalsbychromosome_step",
GenerateIntervalsByChromosome(
reference=None,
)
)
wf.output("out_regions", source=generateintervalsbychromosome_step.out_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 GenerateIntervalsByChromosome:
.. code-block:: bash
# user inputs
janis inputs GenerateIntervalsByChromosome > inputs.yaml
**inputs.yaml**
.. code-block:: yaml
reference: reference.fasta
5. Run GenerateIntervalsByChromosome with:
.. code-block:: bash
janis run [...run options] \
--inputs inputs.yaml \
GenerateIntervalsByChromosome
Information
------------
:ID: ``GenerateIntervalsByChromosome``
:URL: *No URL to the documentation was provided*
:Versions: v0.1.0
:Container: python:3.8.1
:Authors: Michael Franklin
:Citations: None
:Created: 2020-10-19 00:00:00
:Updated: 2020-10-19 00:00:00
Outputs
-----------
=========== ========== ===============
name type documentation
=========== ========== ===============
out_regions Array<bed>
=========== ========== ===============
Additional configuration (inputs)
---------------------------------
=============== ======================= =========================================================================
name type documentation
=============== ======================= =========================================================================
reference FastDict FASTA reference with ^.dict reference
prefix Optional<String> contig prefix, default 'chr'
allowed_contigs Optional<Array<String>> Limits allowed_contigs to a list, this defaults of Human CHRs, 1-23,X,Y,Z
max_size Optional<Integer> Max size of interval, maybe 5000 for VarDict.
overlap Optional<Integer> Consider indels spanning regions, so choose
single_file Optional<Boolean> Produce a SINGLE .bed file with all the listed regions
=============== ======================= =========================================================================