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Add requirements for container images to run with Nextflow #3586

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4 changes: 4 additions & 0 deletions docs/container.rst
Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,10 @@ platform that supports a container runtime. Furthermore, the same pipeline can b
executed with any of the supported container runtimes, depending on which runtimes are available
in the target compute environment.

.. note::
When creating your container image to use with Nextflow make sure it includes Bash (3.x or later) and ``ps`` are installed in your
image, along with other tools required for collecting metrics (See the list :ref:`here <trace-required-packages>`). Also, Bash should be available on the path `/bin/bash` and it should be the container entry-point.

.. _container-charliecloud:

Charliecloud
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2 changes: 2 additions & 0 deletions docs/tracing.rst
Original file line number Diff line number Diff line change
Expand Up @@ -136,6 +136,8 @@ and many other metrics. You can see an example below:

.. image:: images/report-tasks-min.png

.. _trace-required-packages:

.. note::
Nextflow collects these metrics through a background process for each job in the target environment.
Make sure the following tools are available in the environment where tasks are executed: ``awk``, ``date``, ``grep``, ``ps``, ``sed``, ``tail``, ``tee``.
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