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parsefastqcadaptors.rst
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parsefastqcadaptors.rst
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:orphan:
Parse FastQC Adaptors
===========================================
``ParseFastqcAdaptors`` · *1 contributor · 1 version*
Parse overrepresented region and lookup in Cutadapt table
Quickstart
-----------
.. code-block:: python
from janis_bioinformatics.tools.pmac.parsefastqc.v0_1_0 import ParseFastqcAdaptors
wf = WorkflowBuilder("myworkflow")
wf.step(
"parsefastqcadaptors_step",
ParseFastqcAdaptors(
fastqc_datafiles=None,
)
)
wf.output("adaptor_sequences", source=parsefastqcadaptors_step.adaptor_sequences)
*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 ParseFastqcAdaptors:
.. code-block:: bash
# user inputs
janis inputs ParseFastqcAdaptors > inputs.yaml
**inputs.yaml**
.. code-block:: yaml
fastqc_datafiles:
- fastqc_datafiles_0
- fastqc_datafiles_1
5. Run ParseFastqcAdaptors with:
.. code-block:: bash
janis run [...run options] \
--inputs inputs.yaml \
ParseFastqcAdaptors
Information
------------
:ID: ``ParseFastqcAdaptors``
:URL: *No URL to the documentation was provided*
:Versions: v0.1.0
:Container: python:3.8.1
:Authors: Michael Franklin
:Citations: None
:Created: 2020-01-07 00:00:00
:Updated: 2020-02-14 00:00:00
Outputs
-----------
================= ============= ===============
name type documentation
================= ============= ===============
adaptor_sequences Array<String>
================= ============= ===============
Additional configuration (inputs)
---------------------------------
======================== ============== ==========================================================================================
name type documentation
======================== ============== ==========================================================================================
fastqc_datafiles Array<File>
cutadapt_adaptors_lookup Optional<File> Specifies a file which contains the list of adapter sequences which will
be explicity searched against the library. The file must contain sets of named adapters in
the form name[tab]sequence. Lines prefixed with a hash will be ignored.
======================== ============== ==========================================================================================