From df4b5135c371b0b1ce1bf1b1db6e9a0783ccc821 Mon Sep 17 00:00:00 2001 From: Wolfgang Maier Date: Wed, 31 Jan 2024 18:50:40 +0100 Subject: [PATCH] Some improvements to Running Galaxy workflows - Renamed chapter "Interacting with Galaxy workflows" since it's covering a lot more than just planemo run. - Introduced a few, new subheadings - Hopefully improved explanation of workflow testing with planemo test --- docs/_running_intro.rst | 22 +++++++++++++++++----- docs/running.rst | 4 ++-- 2 files changed, 19 insertions(+), 7 deletions(-) diff --git a/docs/_running_intro.rst b/docs/_running_intro.rst index a868ee22e..e4427dd08 100644 --- a/docs/_running_intro.rst +++ b/docs/_running_intro.rst @@ -28,6 +28,9 @@ the ``Number of lines`` parameter) are randomly selected. If you want to view it in the Galaxy interface, you can do so with the command ``planemo workflow_edit tutorial.ga``. +Running a workflow +-------------------------------- + The simplest way to run a workflow with planemo is on a locally hosted Galaxy instance, just like executing a tool test with ``planemo test``. This can be achieved with the command @@ -71,7 +74,14 @@ of the user's choice. The full list of engines provided by Galaxy is: ``galaxy`` (the default, used in the first example above), ``docker_galaxy``, ``cwltool``, ``toil`` and ``external_galaxy``. -As a final example to demonstrate workflow testing, try: +Testing a workflow +-------------------------------- + +Testing a workflow can be thought of as an extension of running a workflow where, +after the run finishes, planemo asserts specified expectations about defined outputs. +Workflow tests, like tool tests, are performed with ``planemo test``. + +As an example, try: :: @@ -100,11 +110,13 @@ If you inspect its contents: path: "data/output.txt" -you see that the job parameters are defined identically to the ``tutorial-job.yml`` -file, with the addition of an output. For the test to pass, the output file -produced by the workflow must be identical to that stored in ``data/output.txt``. +you see that the ``job`` parameters, used to run the workflow, are defined identically to the +``tutorial-job.yml`` file, but that the test definition has an additional ``outputs`` section. +For the test to pass, the output file produced by the workflow must be identical to that stored in ``data/output.txt``. + +More details about workflow testing can be found in the dedicated `Test Format `__ chapter. -The three commands above demonstrate the basics of workflow execution with +The examples above demonstrate the basics of workflow execution with Planemo. For large scale workflow execution, however, it's likely that you would prefer to use the more extensive resources provided by a public Galaxy server, rather than running on a local instance. The tutorial therefore now turns to the diff --git a/docs/running.rst b/docs/running.rst index e130d373a..7e90db8a9 100644 --- a/docs/running.rst +++ b/docs/running.rst @@ -1,5 +1,5 @@ ==================================== -Running Galaxy workflows +Interacting with Galaxy workflows ==================================== Planemo offers a number of convenient commands for working with Galaxy @@ -20,4 +20,4 @@ the ``planemo run`` command, which allows Galaxy tools and workflows to be executed simply via the command line. .. include:: _running_intro.rst -.. include:: _running_external.rst \ No newline at end of file +.. include:: _running_external.rst