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Merge pull request #485 from ewels/rename-ewels-multiqc
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Rename ewels/MegaQC -> MultiQC/MegaQC
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ewels authored Dec 19, 2023
2 parents cf073f0 + 5000d45 commit d1c2ea3
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2 changes: 1 addition & 1 deletion .github/workflows/publish_docs.yaml
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Expand Up @@ -41,7 +41,7 @@ jobs:
# TODO: We could also build latex & PDF documentation and upload them as artifacts

- name: Deploy
if: ${{ github.ref == 'refs/heads/master' }}
if: ${{ github.ref == 'refs/heads/main' }}
uses: peaceiris/actions-gh-pages@v3
with:
github_token: ${{ secrets.GITHUB_TOKEN }}
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24 changes: 12 additions & 12 deletions CHANGELOG.rst
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Expand Up @@ -19,9 +19,9 @@ Development
* Fix a bug in pytest where we used `scope` as a positional argument
* Update the SubFactoryList to a new version that works with newer FactoryBoy versions

.. _[#430]: https://github.com/ewels/MegaQC/issues/430
.. _[#440]: https://github.com/ewels/MegaQC/pull/440
.. _[#433]: https://github.com/ewels/MegaQC/pull/433
.. _[#430]: https://github.com/MultiQC/MegaQC/issues/430
.. _[#440]: https://github.com/MultiQC/MegaQC/pull/440
.. _[#433]: https://github.com/MultiQC/MegaQC/pull/433

=======

Expand Down Expand Up @@ -87,12 +87,12 @@ Internal Changes
- Many and more dependency updates


.. _[#69]: https://github.com/ewels/MegaQC/issues/69
.. _[#138]: https://github.com/ewels/MegaQC/issues/138
.. _[#139]: https://github.com/ewels/MegaQC/issues/139
.. _[#140]: https://github.com/ewels/MegaQC/issues/140
.. _[#148]: https://github.com/ewels/MegaQC/issues/148
.. _[#156]: https://github.com/ewels/MegaQC/issues/156
.. _[#170]: https://github.com/ewels/MegaQC/issues/170
.. _[#194]: https://github.com/ewels/MegaQC/issues/194
.. _[#443]: https://github.com/ewels/MegaQC/pull/443
.. _[#69]: https://github.com/MultiQC/MegaQC/issues/69
.. _[#138]: https://github.com/MultiQC/MegaQC/issues/138
.. _[#139]: https://github.com/MultiQC/MegaQC/issues/139
.. _[#140]: https://github.com/MultiQC/MegaQC/issues/140
.. _[#148]: https://github.com/MultiQC/MegaQC/issues/148
.. _[#156]: https://github.com/MultiQC/MegaQC/issues/156
.. _[#170]: https://github.com/MultiQC/MegaQC/issues/170
.. _[#194]: https://github.com/MultiQC/MegaQC/issues/194
.. _[#443]: https://github.com/MultiQC/MegaQC/pull/443
10 changes: 4 additions & 6 deletions README.rst
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Expand Up @@ -20,7 +20,7 @@ MegaQC is a web application that you can install and run on your own
network. It collects and visualises data parsed by MultiQC across multiple runs.
The MegaQC home page looks something like this:

.. figure:: https://raw.githubusercontent.com/ewels/MegaQC/master/docs/source/images/megaqc_homepage.png
.. figure:: https://raw.githubusercontent.com/MultiQC/MegaQC/main/docs/source/images/megaqc_homepage.png
:alt: MegaQC homepage

Screenshot of the MegaQC home page.
Expand All @@ -37,11 +37,9 @@ to learn how to install, deploy and use MegaQC.
.. _MultiQC website: http://multiqc.info
.. _GitHub repository: https://github.com/ewels/MultiQC

.. |MegaQC| image:: https://raw.githubusercontent.com/ewels/MegaQC/master/megaqc/static/img/MegaQC_logo.png
.. |Docker| image:: https://img.shields.io/docker/automated/ewels/megaqc.svg?style=flat-square
:target: https://hub.docker.com/r/ewels/megaqc/
.. |Build Status| image:: https://travis-ci.org/ewels/MegaQC.svg?branch=master
:target: https://travis-ci.org/ewels/MegaQC
.. |MegaQC| image:: https://raw.githubusercontent.com/MultiQC/MegaQC/main/megaqc/static/img/MegaQC_logo.png
.. |Docker| image:: https://img.shields.io/docker/automated/multiqc/megaqc.svg?style=flat-square
:target: https://hub.docker.com/r/multiqc/megaqc/
.. |Gitter| image:: https://img.shields.io/badge/gitter-%20join%20chat%20%E2%86%92-4fb99a.svg?style=flat-square
:target: https://gitter.im/ewels/MegaQC
.. |Documentation| image:: https://img.shields.io/badge/Documentation-passing-passing
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2 changes: 1 addition & 1 deletion deployment/docker-compose.yml
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Expand Up @@ -2,7 +2,7 @@ version: "3.7"

services:
megaqc:
image: ewels/megaqc
image: multiqc/megaqc
build: ..
volumes:
# Share the static files via a volume
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6 changes: 3 additions & 3 deletions docs/source/_templates/index.html
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Expand Up @@ -26,8 +26,8 @@ <h1><a href="index.html"><img src="_static/images/MegaQC_logo_darkbg.svg" title=
<li class="current"><a href="index.html">Home</a></li>
<li><a href="docs/index.html" title="Read the MegaQC documentation">Docs</a></li>
<li><a href="http://multiqc.info/" target="_blank" title="Find out more about MultiQC, which MegaQC relies upon">MultiQC</a></li>
<li><a href="https://gitter.im/ewels/MegaQC" target="_blank" title="Get help by chatting with the developers">Gitter</a></li>
<li><a href="https://github.com/ewels/MegaQC" target="_blank" title="View the code on GitHub">GitHub</a></li>
<li><a href="https://gitter.im/MultiQC/MegaQC" target="_blank" title="Get help by chatting with the developers">Gitter</a></li>
<li><a href="https://github.com/MultiQC/MegaQC" target="_blank" title="View the code on GitHub">GitHub</a></li>
</ul>
</nav>

Expand Down Expand Up @@ -186,7 +186,7 @@ <h2>Still not sure?</h2>
<ul class="actions">
<li><a href="docs/index.html" class="button style2">Read the docs</a></li>
<li><a href="#" class="button style1">Try a live demo</a></li>
<li><a href="https://github.com/ewels/MegaQC" target="_blank" class="button style2">See the code</a></li>
<li><a href="https://github.com/MultiQC/MegaQC" target="_blank" class="button style2">See the code</a></li>
</ul>
</header>

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10 changes: 5 additions & 5 deletions docs/source/conf.py
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Expand Up @@ -67,9 +67,9 @@
"display_github": True,
# Set the following variables to generate the resulting github URL for each page.
# Format Template: https://{{ github_host|default("github.com") }}/{{ github_user }}/{{ github_repo }}/blob/{{ github_version }}{{ conf_py_path }}{{ pagename }}{{ suffix }}
"github_user": "ewels",
"github_user": "MultiQC",
"github_repo": "MegaQC",
"github_version": "master/docs",
"github_version": "main/docs",
"conf_py_path": "/source/",
}

Expand All @@ -95,7 +95,7 @@ def find_source():
filename = "megaqc/%s#L%d-L%d" % find_source()
except Exception:
filename = info["module"].replace(".", "/") + ".py"
tag = "master"
# TODO use this after the first release: tag = 'master' if 'dev' in release else ('v' + release)
tag = "main"
# TODO use this after the first release: tag = 'main' if 'dev' in release else ('v' + release)

return "https://github.com/ewels/megaqc/blob/%s/%s" % (tag, filename)
return "https://github.com/MultiQC/MegaQC/blob/%s/%s" % (tag, filename)
22 changes: 11 additions & 11 deletions docs/source/docs/dev/backend.rst
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Expand Up @@ -13,7 +13,7 @@ will likely be SQLite.

Database models are located in `model/models.py`_ and `user/models.py`_.

Database schema migrations
Database schema migrations
^^^^^^^^^^^^^^^^^^^^^^^^^^^^

You need to generate a new migration whenever the database schema (ie
Expand Down Expand Up @@ -61,16 +61,16 @@ be done inside `test_api.py`_, which tests all REST API endpoints.

.. _flask: https://www.palletsprojects.com/p/flask/
.. _SQLAlchemy: https://docs.sqlalchemy.org/
.. _model/models.py: https://github.com/ewels/MegaQC/blob/master/megaqc/model/models.py
.. _user/models.py: https://github.com/ewels/MegaQC/blob/master/megaqc/user/models.py
.. _megaqc/api: https://github.com/ewels/MegaQC/tree/master/megaqc/api
.. _megaqc/rest_api: https://github.com/ewels/MegaQC/tree/master/megaqc/rest_api
.. _views.py: https://github.com/ewels/MegaQC/blob/master/megaqc/rest_api/views.py
.. _model/models.py: https://github.com/MultiQC/MegaQC/blob/main/megaqc/model/models.py
.. _user/models.py: https://github.com/MultiQC/MegaQC/blob/main/megaqc/user/models.py
.. _megaqc/api: https://github.com/MultiQC/MegaQC/tree/main/megaqc/api
.. _megaqc/rest_api: https://github.com/MultiQC/MegaQC/tree/main/megaqc/rest_api
.. _views.py: https://github.com/MultiQC/MegaQC/blob/main/megaqc/rest_api/views.py
.. _flapison: https://github.com/TMiguelT/flapison
.. _schemas.py: https://github.com/ewels/MegaQC/tree/master/megaqc/rest_api/schemas.py
.. _public/views.py: https://github.com/ewels/MegaQC/tree/master/megaqc/public/views.py
.. _user/views.py: https://github.com/ewels/MegaQC/tree/master/megaqc/user/views.py
.. _schemas.py: https://github.com/MultiQC/MegaQC/tree/main/megaqc/rest_api/schemas.py
.. _public/views.py: https://github.com/MultiQC/MegaQC/tree/main/megaqc/public/views.py
.. _user/views.py: https://github.com/MultiQC/MegaQC/tree/main/megaqc/user/views.py
.. _Jinja2: https://jinja.palletsprojects.com/en/2.11.x/
.. _frontend: ./frontend.md
.. _python_tests: https://github.com/ewels/MegaQC/tree/master/tests
.. _test_api.py: https://github.com/ewels/MegaQC/tree/master/megaqc/api/test_api.py
.. _python_tests: https://github.com/MultiQC/MegaQC/tree/main/tests
.. _test_api.py: https://github.com/MultiQC/MegaQC/tree/main/megaqc/api/test_api.py
8 changes: 4 additions & 4 deletions docs/source/docs/dev/documentation.rst
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Expand Up @@ -10,8 +10,8 @@ Building the documentation locally
The MegaQC documentation requires

1. An installation of MegaQC to fetch the API endpoints and the Click commands.
2. All dependencies specified in the `docs requirements.txt <https://github.com/ewels/MegaQC/blob/master/docs/requirements.txt>`_.
Install them by invoking: ``pip install -r docs/requirements.txt``.
2. All dependencies specified in the `docs requirements.txt <https://github.com/MultiQC/MegaQC/blob/main/docs/requirements.txt>`_.
Install them by invoking: ``pip install -r docs/requirements.txt``.

After having installed all requirements run ``make api-docs && make html`` in the ``docs`` directory.
The generated ``html`` files are found in the ``docs/_build/html`` subfolder.
Expand All @@ -20,7 +20,7 @@ Simply open a generated ``html`` file in your favorite browser to read the docum
Publishing the documentation
---------------------------------

On pushes to the ``master`` branch, the documentation is automatically built and pushed
On pushes to the ``main`` branch, the documentation is automatically built and pushed
to the ``gh-pages`` branch. The static html files on this branch are then deployed
to Github Pages and displayed to the outside world.
All of this is done with the `Publish Docs Github Actions workflow <https://github.com/ewels/MegaQC/blob/master/.github/workflows/publish_docs.yaml>`.
All of this is done with the `Publish Docs Github Actions workflow <https://github.com/MultiQC/MegaQC/blob/main/.github/workflows/publish_docs.yaml>`.
8 changes: 4 additions & 4 deletions docs/source/docs/dev/frontend.rst
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Expand Up @@ -22,7 +22,7 @@ Note that all new pages going forward should be written using React, to
improve the maintainability of the frontend.

.. _React: https://reactjs.org/
.. _templates: https://github.com/ewels/MegaQC/tree/master/megaqc/templates
.. _static: https://github.com/ewels/MegaQC/tree/master/megaqc/static
.. _react.html: https://github.com/ewels/MegaQC/tree/master/megaqc/templates/public/react.html
.. _src: https://github.com/ewels/MegaQC/tree/master/src
.. _templates: https://github.com/MultiQC/MegaQC/tree/main/megaqc/templates
.. _static: https://github.com/MultiQC/MegaQC/tree/main/megaqc/static
.. _react.html: https://github.com/MultiQC/MegaQC/tree/main/megaqc/templates/public/react.html
.. _src: https://github.com/MultiQC/MegaQC/tree/main/src
2 changes: 1 addition & 1 deletion docs/source/docs/index.rst
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Expand Up @@ -23,4 +23,4 @@ Indices and tables
* :ref:`modindex`
* :ref:`search`

.. |MegaQC| image:: https://raw.githubusercontent.com/ewels/MegaQC/master/megaqc/static/img/MegaQC_logo.png
.. |MegaQC| image:: https://raw.githubusercontent.com/MultiQC/MegaQC/main/megaqc/static/img/MegaQC_logo.png
2 changes: 1 addition & 1 deletion docs/source/docs/installation/installation_dev.rst
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Expand Up @@ -17,7 +17,7 @@ If you’re doing development work, you need access to the source code

.. code:: bash
git clone https://github.com/ewels/MegaQC
git clone https://github.com/MultiQC/MegaQC/
2. Install Dependencies
------------------------------------------------
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44 changes: 22 additions & 22 deletions docs/source/docs/installation/installation_docker.rst
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Expand Up @@ -14,10 +14,10 @@ The MegaQC Docker container
Overview
~~~~~~~~~~

The MegaQC container is based on the `Node container <https://hub.docker.com/_/node>`_
The MegaQC container is based on the `Node container <https://hub.docker.com/_/node>`_
to compile all Javascript scripts and the `Gunicorn Flask container <https://hub.docker.com/r/tiangolo/meinheld-gunicorn-flask/dockerfile>`_
providing Gunicorn, Flask and MegaQC preconfigured for production deployments.
The `Gunicorn Flask <https://hub.docker.com/r/tiangolo/meinheld-gunicorn-flask/dockerfile>`_ container
The `Gunicorn Flask <https://hub.docker.com/r/tiangolo/meinheld-gunicorn-flask/dockerfile>`_ container
is also the one spinning up the final server.

Pulling the docker image from dockerhub
Expand All @@ -27,7 +27,7 @@ To run MegaQC with docker, simply use the following command:

.. code:: bash
docker run -p 80:80 ewels/megaqc
docker run -p 80:80 multiqc/megaqc
This will pull the latest image from `dockerhub`_ and run MegaQC on port 80.

Expand All @@ -42,21 +42,21 @@ MegaQC code from GitHub. Simply cd to the MegaQC root directory and run

.. code:: bash
docker build . -t ewels/megaqc
docker build . -t multiqc/megaqc
You can then run MegaQC as described above:

.. code:: bash
docker run -p 80:80 ewels/megaqc
docker run -p 80:80 multiqc/megaqc
Configuration
~~~~~~~~~~~~~~~

Besides the sections below it is also recommended to read the
Besides the sections below it is also recommended to read the
`Gunicorn Flask container documentation <https://github.com/tiangolo/meinheld-gunicorn-flask-docker>`_,
which explains how to customize the ``host`` IP where Gunicorn listens
to requests, the ``port`` the container should listen on and ``bind``, the actual
to requests, the ``port`` the container should listen on and ``bind``, the actual
host and port passed to gunicorn, let alone custom Gunicorn configuration files.

Environment variables
Expand All @@ -83,21 +83,21 @@ Running MegaQC for example with a custom database password works as follows:

.. code-block:: bash
docker run -e DB_PASS=someotherpassword ewels/megaqc
docker run -e DB_PASS=someotherpassword multiqc/megaqc
Furthermore, be aware that the default latest tag will typically be a development version
and may not be very stable. You can specify a tagged version to run a release instead:

.. code:: bash
docker run -p 80:80 ewels/megaqc:v0.1
docker run -p 80:80 multiqc/megaqc:v0.2.0
Also note that docker will use a local version of the image if it
exists. To pull the latest version of MegaQC use the following command:

.. code:: bash
docker pull ewels/megaqc
docker pull multiqc/megaqc
Using persistent data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Expand All @@ -117,13 +117,13 @@ To create or re-use a docker volume named ``pg_data``:

.. code:: bash
docker run -p 80:80 -v pg_data:/usr/local/lib/postgresql ewels/megaqc
docker run -p 80:80 -v pg_data:/usr/local/lib/postgresql multiqc/megaqc
The same can be done for a log directory volume called ``pg_logs``

.. code:: bash
docker run -p 80:80 -v pg_data:/usr/local/lib/postgresql -v pg_logs:/var/log/postgresql ewels/megaqc
docker run -p 80:80 -v pg_data:/usr/local/lib/postgresql -v pg_logs:/var/log/postgresql multiqc/megaqc
If you did not specify a volume name, docker will have given it a long
hex string as a unique name. If you do not use volumes frequently, you
Expand Down Expand Up @@ -181,7 +181,7 @@ on ``localhost:5432``, looks as follows:

.. code:: bash
docker run --network="host" -p 5432 ewels/megaqc
docker run --network="host" -p 5432 multiqc/megaqc
Note that by default ``localhost=127.0.0.1``.

Expand All @@ -199,15 +199,15 @@ Overview

The `docker-compose`_ configuration can be accessed in the `deployment folder`_.
The docker-compose configuration provides the :ref:`megaqc_docker_container`,
a `postgres container <https://hub.docker.com/_/postgres>`_ for the SQL database
a `postgres container <https://hub.docker.com/_/postgres>`_ for the SQL database
and a `nginx container <https://hub.docker.com/_/nginx>`_ for the reverse proxy setup.

Usage
~~~~~~~~

Inside the `deployment folder`_ the `docker-compose`_ configuration
together with the associated `.env <https://github.com/ewels/MegaQC/blob/master/deployment/.env>`_ file
are found. To spin up all containers simply run from inside the `deployment folder <https://github.com/ewels/MegaQC/blob/master/deployment>`_:
together with the associated `.env <https://github.com/MultiQC/MegaQC/blob/main/deployment/.env>`_ file
are found. To spin up all containers simply run from inside the `deployment folder <https://github.com/MultiQC/MegaQC/blob/main/deployment>`_:

.. code:: bash
Expand All @@ -229,19 +229,19 @@ Environment variables
^^^^^^^^^^^^^^^^^^^^^^^^^^

The default environment variables for MegaQC used when starting the :ref:`megaqc_docker_container`
are defined inside the `.env <https://github.com/ewels/MegaQC/blob/master/deployment/.env>`_ file.
are defined inside the `.env <https://github.com/MultiQC/MegaQC/blob/main/deployment/.env>`_ file.
Simply edit the file and the new environment variables will be passed to the :ref:`megaqc_docker_container`.

Further runtime arguments
^^^^^^^^^^^^^^^^^^^^^^^^^^^

Further runtime arguments can be added to a
Further runtime arguments can be added to a
`command section <https://docs.docker.com/compose/compose-file/#command>`_
inside the `docker-compose`_ configuration file.

.. _deployment_folder: https://github.com/ewels/MegaQC/blob/master/deployment
.. _docker-compose: https://github.com/ewels/MegaQC/blob/master/deployment/docker-compose.yml
.. _dockerhub: https://hub.docker.com/r/ewels/megaqc/
.. _deployment_folder: https://github.com/MultiQC/MegaQC/blob/main/deployment
.. _docker-compose: https://github.com/MultiQC/MegaQC/blob/main/deployment/docker-compose.yml
.. _dockerhub: https://hub.docker.com/r/multiqc/megaqc/

HTTPS
~~~~~
Expand All @@ -256,4 +256,4 @@ Then, edit these lines to the full filepath of the respective ``.crt`` and ``.ke
CRT_PATH=./nginx-selfsigned.crt
KEY_PATH=./nginx-selfsigned.key
After this, run the stack as described above, and then you should be able to access MegaQC on ``https://your_hostname``.
After this, run the stack as described above, and then you should be able to access MegaQC on ``https://your_hostname``.
8 changes: 4 additions & 4 deletions docs/source/docs/installation/installation_prod.rst
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Expand Up @@ -2,8 +2,8 @@ Production
=============

This section explains how to set up a production environment without
the usage of container technologies. If you want to run MegaQC in a
containerized environment please refer to :ref:`docker_installation`.
the usage of container technologies. If you want to run MegaQC in a
containerized environment please refer to :ref:`docker_installation`.

1. Install the MegaQC package
-----------------------------
Expand Down Expand Up @@ -169,5 +169,5 @@ If you run an older OS, ensure that the package is installed.

.. _Python MySQL connector: https://dev.mysql.com/downloads/connector/python/2.1.html
.. _PyPI package: https://pypi.python.org/pypi/mysql-connector-python/2.0.4
.. _create an issue: https://github.com/ewels/MegaQC/issues/new
.. _deployment_folder: https://github.com/ewels/MegaQC/blob/master/deployment
.. _create an issue: https://github.com/MultiQC/MegaQC/issues/new
.. _deployment_folder: https://github.com/MultiQC/MegaQC/blob/main/deployment
4 changes: 2 additions & 2 deletions docs/source/docs/troubleshooting.rst
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Expand Up @@ -18,9 +18,9 @@ Usage

- When creating a violin plot I get an error.

- This is a known issue: https://github.com/ewels/MegaQC/issues/31
- This is a known issue: https://github.com/MultiQC/MegaQC/issues/31

- TypeError: '<' not supported between instances of 'NoneType' and 'float' when trying to compare data

- This is a known issue: https://github.com/ewels/MegaQC/issues/156
- This is a known issue: https://github.com/MultiQC/MegaQC/issues/156
- Please ensure that your reports do not have missing fields
2 changes: 1 addition & 1 deletion megaqc/templates/footer.html
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Expand Up @@ -6,7 +6,7 @@
<p>
<a href="http://multiqc.info/db" target="_blank">MegaQC v{{ version }}</a>
- Written by Phil Ewels, Denis Moreno, Michael Milton, Tor Solli-Nowlan and Lukas Heumos,
available on <a href="https://github.com/ewels/MegaQC" target="_blank">GitHub</a>.
available on <a href="https://github.com/MultiQC/MegaQC" target="_blank">GitHub</a>.
</p>
<p>
MegaQC uses
Expand Down
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