chilin2
=======

extend your pipeline
---------------------
ChiLin is written with python and shell, it's easy to extend to fit your need.

* in chilin2/modules/, `mkdir chilin2/modules/my_pipe && touch chilin2/modules/my_pipe/__init__.py`
* write your command into chilin2/modules/my_pipe/__init__.py like following:

.. code-block:: python

    from samflow.command import ShellCommand
    from samflow.workflow import attach_back
    def tail(workflow, conf):
        tail = attach_back(workflow,
        ShellCommand(
        """{tool} -50 {input[peaks]} > {output[p]}
        """,
        tool = "sort",
        input = {"peaks": conf.prefix + "_sort_peaks.narrowPeak"},
        output = {"p":conf.prefix + "_sort_peaks_tail_50.narrowPeak"},
        name = "get tail lines"))


.. code-block:: python

    from chilin2.modules.my_pipe import tail
    ....
    #at line 349
    if need_run(13):
       bld.build(tail)


:mod:`chilin2` -- utils package
---------------------------------
.. automodule:: chilin2

.. automodule:: chilin2.modules

.. automodule:: chilin2.modules.bwa

.. automodule:: chilin2.modules.config

.. automodule:: chilin2.modules.config.config

.. automodule:: chilin2.modules.config.helpers

.. automodule:: chilin2.modules.fastqc.dc

.. automodule:: chilin2.modules.fastqc.qc

.. automodule:: chilin2.modules.fastqc.tex

.. automodule:: chilin2.modules.bwa.dc

.. automodule:: chilin2.modules.bwa.qc

.. automethod:: chilin2.modules.bwa.dc.bwa

.. automodule:: chilin2.modules.macs

.. automodule:: chilin2.modules.macs.dc

.. automethod:: chilin2.modules.macs.dc.macs2

.. automodule:: chilin2.modules.ceas

.. automodule:: chilin2.modules.ceas.dc

.. automodule:: chilin2.modules.ceas.qc

.. automodule:: chilin2.modules.frip

.. automodule:: chilin2.modules.frip.dc

.. automodule:: chilin2.modules.frip.qc

.. automodule:: chilin2.modules.library

.. automodule:: chilin2.modules.library.dc

.. automodule:: chilin2.modules.library.qc

.. automodule:: chilin2.modules.enrichment

.. automodule:: chilin2.modules.enrichment.dc

.. automodule:: chilin2.modules.macs2_fragment

.. automodule:: chilin2.modules.macs2_fragment.dc

.. automodule:: chilin2.modules.macs2_fragment.qc

.. automodule:: chilin2.modules.replicates

.. automodule:: chilin2.modules.replicates.dc

.. automodule:: chilin2.modules.replicates.qc

.. automodule:: chilin2.modules.conservation

.. automodule:: chilin2.modules.conservation.dc

.. automodule:: chilin2.modules.conservation.qc

.. automodule:: chilin2.modules.contamination

.. automodule:: chilin2.modules.contamination.dc

.. automodule:: chilin2.modules.contamination.qc

.. automodule:: chilin2.modules.contamination.tex

.. automodule:: chilin2.modules.regulatory

.. automodule:: chilin2.modules.regulatory.dc

.. automodule:: chilin2.modules.mdseqpos

.. automodule:: chilin2.modules.mdseqpos.dc

.. automodule:: chilin2.modules.mdseqpos.qc

.. automodule:: chilin2.modules.mdseqpos.tex

.. automodule:: chilin2.modules.summary

.. automodule:: chilin2.modules.summary.qc_json_summary

.. automodule:: chilin2.modules.summary.qc_summary_table

:mod:`samflow` -- utils package
---------------------------------

.. automodule:: samflow

.. autoclass:: samflow.command.ShellCommand

.. autoclass:: samflow.workflow.Workflow

.. autoclass:: samflow.command.PythonCommand