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#snakemakehackathon2025

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Christian Meesters<p>Busy year:</p><p>- Workflow programming for Data Analysis on <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>HPC</span></a> Systems (Course in Mainz in January): ✅ <br>- Same Course in Dresden (February) ✅ <br>- <a href="https://fediscience.org/tags/SnakemakeHackathon2025" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>SnakemakeHackathon2025</span></a> at the CERN in March: ✅ <br>- upcoming: <a href="https://fediscience.org/tags/OpenScience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>OpenScience</span></a> Retreat (no hashtag, yet?) in April<br>- International Supercomputing Conference in June (so, <span class="h-card" translate="no"><a href="https://mast.hpc.social/@boegel" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>boegel</span></a></span>, I will be there, after all and hope to meet people from <span class="h-card" translate="no"><a href="https://fosstodon.org/@irods" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>irods</span></a></span>, too ; will you be there folks from <a href="https://fediscience.org/tags/iRODS" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>iRODS</span></a> ?)<br>- German Conference for <a href="https://fediscience.org/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Bioinformatics</span></a> and NHR Conference in September</p><p>And I do not know whether this will be all. I have a nagging feeling there is more to come 😉</p>
Christian Meesters<p>The <a href="https://fediscience.org/tags/SnakemakeHackathon2025" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>SnakemakeHackathon2025</span></a> just induced another collaboration for me!</p><p>It is always good to work along with like-minded people, interested in <a href="https://fediscience.org/tags/ReproducibleComputing" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>ReproducibleComputing</span></a>, <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>HPC</span></a> and <a href="https://fediscience.org/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Bioinformatics</span></a> </p><p><a href="https://fediscience.org/tags/OpenScience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>OpenScience</span></a></p>
Johannes Köster<p>Today, the <a href="https://fosstodon.org/tags/SnakemakeHackathon2025" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>SnakemakeHackathon2025</span></a> at <span class="h-card" translate="no"><a href="https://quey.org/@CERN" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>CERN</span></a></span> has ended with the release of Snakemake 9.0! Huge thanks to the amazing participants and all organizers! In total there were 19 new releases within the ecosystem, including hundreds of new features and bug fixes for Snakemake and its plugins!</p>
Christian Meesters<p>Today at the <a href="https://fediscience.org/tags/SnakemakeHackathon2025" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>SnakemakeHackathon2025</span></a>:</p><p>We did a tour around the CERN!</p><p>But, of course, work was done, too! On cvmfs support for software deployment, many core features, improved metadata reporting, more stable SLURM executor, etc. etc. etc. Soon you will read more. 😉</p>
Johannes Köster<p>The third day of the <a href="https://fosstodon.org/tags/SnakemakeHackathon2025" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>SnakemakeHackathon2025</span></a> at <span class="h-card" translate="no"><a href="https://quey.org/@CERN" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>CERN</span></a></span> is over. 11 fantastic pull requests have been merged, fixing various bugs, enabling custom logging, improving the docs, and the expressiveness of the language. <a href="https://snakemake.github.io" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="">snakemake.github.io</span><span class="invisible"></span></a></p>
Christian Meesters<p>Today is the day of closed pull request for <a href="https://fediscience.org/tags/Snakemake" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Snakemake</span></a>. The <a href="https://fediscience.org/tags/SnakemakeHackathon2025" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>SnakemakeHackathon2025</span></a> participants worked at full speed!</p><p>We decided to write a white-paper summarizing our achievements rather than posting individual things. Suffice to say, that also the documentation made a great leap towards better readability!</p><p><a href="https://fediscience.org/tags/OpenScience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>OpenScience</span></a> <a href="https://fediscience.org/tags/ReproducibleComputing" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>ReproducibleComputing</span></a> <a href="https://fediscience.org/tags/ReproducibleResearch" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>ReproducibleResearch</span></a></p>
Johannes Köster<p>The second day of the <a href="https://fosstodon.org/tags/SnakemakeHackathon2025" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>SnakemakeHackathon2025</span></a> is over. Today I have merged 11 fantastic pull requests in the in main snakemake repo alone. And we have our first <a href="https://fosstodon.org/tags/Snakemake" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Snakemake</span></a> release during the hackathon, adding integration with xonsh for scripting and helpers for extracting params from input files.</p>
Christian Meesters<p><a href="https://fediscience.org/tags/SnakemakeHackathon2025" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>SnakemakeHackathon2025</span></a> ! We started!</p><p>At the CERN for better <a href="https://fediscience.org/tags/ReproducibleComputing" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>ReproducibleComputing</span></a> and <a href="https://fediscience.org/tags/ReproducibleResearch" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>ReproducibleResearch</span></a> .</p>
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