Configuration
=============

Shellflow can be configured GridEngine options or other options with
TOML file.

Command
-------

RegExp
~~~~~~

If a command to run is matched to a regular expression, options listed
in below will be applied.

RunImmediate
~~~~~~~~~~~~

If this option is setted to true, command will be run immediately
without using job scheduler.

DontInheirtPath
~~~~~~~~~~~~~~~

If this option is setted to true, Shellflow will not inheirt ``PATH``
and ``LD_LIBRARY_PATH`` when running with job scheduler.

SGEOption
~~~~~~~~~

This options will be passed to Univa/Sun Grid Engine ``qsub``.

Configuration Example
---------------------

.. code:: toml

    [[Command]]
    RegExp = "mkdir +(-p +)?[^;&]+"
    RunImmediate = true

    [[Command]]
    RegExp = "example_dont_inheirt_path"
    DontInheirtPath = true

    [[Command]]
    RegExp = "gatk .*"
    SGEOption = ["-l", "s_vmem=20G,mem_req=20G", "-pe", "def_slot", "2"]

    [[Command]]
    RegExp = "samtools .*"
    SGEOption = ["-l", "s_vmem=10G,mem_req=10G", "-pe", "def_slot", "2"]

    [[Command]]
    RegExp = "java .*"
    SGEOption = ["-l", "s_vmem=40G,mem_req=40G"]