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Refs: #195 GenPipes v4.3.2 RN updated
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4.3.1 | ||
4.3.2 |
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:orphan: | ||
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.. _docs_gp_relnote_4_3_2: | ||
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.. spelling:: | ||
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sambamba | ||
genpipes | ||
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GenPipes 4.3.2 Release Notes | ||
============================ | ||
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What's new? | ||
----------- | ||
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This release is mainly a bug-fix release. | ||
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* `Tumor Pair <https://genpipes.readthedocs.io/en/genpipes-v4.3.2/user_guide/pipelines/gp_tumourpair.html>`_: Fixed 'sambamba sort' crashing issues encountered with some tumor pair samples. | ||
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* `DNA Sequencing Pipeline (SV) <https://genpipes.readthedocs.io/en/genpipes-v4.3.2/user_guide/pipelines/gp_dnaseq.html>`_: Several bugs were fixed in this pipeline after we identified and repaired some weakness spots in our testing suite. | ||
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* `RNA Sequencing Pipeline <https://genpipes.readthedocs.io/en/genpipes-v4.3.2/user_guide/pipelines/gp_rnaseq.html>`_: Now allows for batch effect correction (with DESeq2). | ||
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* The "`resources <https://bitbucket.org/mugqic/genpipes/src/master/resources/>`" folder is no more part of the GenPipes 4.3.2 release but remains accessible in our repository. | ||
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Please note that as a consequence, the ``Homo sapiens`` configuration files formerly in ``resources/genomes/config`` folder have been moved to ``pipelines/common ini`` folder. | ||
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* Besides the above mentioned updates, this release includes lots of code clean ups and linting changes. | ||
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Quick! Where can I find it? I can't wait! | ||
------------------------------------------ | ||
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* The latest release for GenPipes version 4.3.2 tarball is in: https://bitbucket.org/mugqic/genpipes/downloads/genpipes-4.3.2.tar.gz | ||
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* The module mugqic/genpipes/4.3.2 is installed on Abacus (MGC), Béluga, Narval, Graham and Cedar Compute Canada clusters. | ||
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* The source code is in bitbucket: https://bitbucket.org/mugqic/genpipes | ||
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* For latest GenPipes documentation, please refer to: https://genpipes.readthedocs.io/ | ||
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Where is the detailed ChangeLog? | ||
================================= | ||
A ChangeLog (`CHANGELOG.md <https://bitbucket.org/mugqic/genpipes/src/master/CHANGELOG.md>`_) is available in the archive as well as in the repository. | ||
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Since we use git, there are many ways to get the details in many formats. | ||
One of our preferred ways is to use a script written by the author of the Ray assembler: Sébastien Boisvert, | ||
which lists the commits by tag and author: | ||
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https://raw.github.com/sebhtml/ray/master/scripts/dump-ChangeLog.sh | ||
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Enjoy our pipelines on the many clusters where they are installed! |