diff --git a/docs/dev_intro.rst b/docs/dev_intro.rst index 33c5c2fa8..4a7f6a32d 100644 --- a/docs/dev_intro.rst +++ b/docs/dev_intro.rst @@ -99,6 +99,9 @@ Usually, you define a :class:`BaseStep ` instance as the values for the ``input:``, ``output:``, etc. sections of your ``Snakefile``. +.. warning:: + By convention your new Workflow step should be instantiated as ``wf = StepClass(...)`` in the ``Snakefile`` during object setup. Otherwise tools including cubi-tk might not be able to detect and parse your step. See existing workflow ``Snakefile`` for reference. + The :class:`BaseStep ` sub class itself uses :class:`BaseStepPart ` sub classes for the implementation of the individual parts. One part might be linking in FASTQ files from the raw input directory or linking from the ``work/`` to the ``output/`` directory. Another part might be the somatic variant calling using mutect or WGS SV calling using Delly2.