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#sciworkflows

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Johannes Köster<p><a href="https://fosstodon.org/tags/Snakemake" class="mention hashtag" rel="tag">#<span>Snakemake</span></a> 8.25.4 has been released with lots of little bug fixes: <a href="https://snakemake.readthedocs.io/en/stable/project_info/history.html" target="_blank" rel="nofollow noopener" translate="no"><span class="invisible">https://</span><span class="ellipsis">snakemake.readthedocs.io/en/st</span><span class="invisible">able/project_info/history.html</span></a> <a href="https://fosstodon.org/tags/sciworkflows" class="mention hashtag" rel="tag">#<span>sciworkflows</span></a> <a href="https://fosstodon.org/tags/reproducibility" class="mention hashtag" rel="tag">#<span>reproducibility</span></a></p>
Johannes Köster<p><a href="https://fosstodon.org/tags/Snakemake" class="mention hashtag" rel="tag">#<span>Snakemake</span></a> 8.20.4 has been released. It provides a massive speedup of job processing, most notable during dry-run. <a href="https://fosstodon.org/tags/sciworkflows" class="mention hashtag" rel="tag">#<span>sciworkflows</span></a> <a href="https://fosstodon.org/tags/reproducibility" class="mention hashtag" rel="tag">#<span>reproducibility</span></a> <a href="https://snakemake.github.io" target="_blank" rel="nofollow noopener" translate="no"><span class="invisible">https://</span><span class="">snakemake.github.io</span><span class="invisible"></span></a></p>
Johannes Köster<p>New <a href="https://fosstodon.org/tags/snakemake_wrappers" class="mention hashtag" rel="tag">#<span>snakemake_wrappers</span></a> release with 17 updates and 1 new wrapper! <a href="https://snakemake-wrappers.readthedocs.io" target="_blank" rel="nofollow noopener" translate="no"><span class="invisible">https://</span><span class="ellipsis">snakemake-wrappers.readthedocs</span><span class="invisible">.io</span></a> <a href="https://fosstodon.org/tags/sciworkflows" class="mention hashtag" rel="tag">#<span>sciworkflows</span></a> <a href="https://fosstodon.org/tags/reproducibility" class="mention hashtag" rel="tag">#<span>reproducibility</span></a></p>
Johannes Köster<p>Lot&#39;s of new <a href="https://fosstodon.org/tags/snakemake" class="mention hashtag" rel="tag">#<span>snakemake</span></a> and <a href="https://fosstodon.org/tags/snakemake" class="mention hashtag" rel="tag">#<span>snakemake</span></a> plugin releases in the last days, with a plethora of bug fixes and small feature improvements. <a href="https://snakemake.github.io" target="_blank" rel="nofollow noopener" translate="no"><span class="invisible">https://</span><span class="">snakemake.github.io</span><span class="invisible"></span></a> <a href="https://fosstodon.org/tags/sciworkflows" class="mention hashtag" rel="tag">#<span>sciworkflows</span></a> <a href="https://fosstodon.org/tags/reproducibility" class="mention hashtag" rel="tag">#<span>reproducibility</span></a></p>
Johannes Köster<p><a href="https://fosstodon.org/tags/snakemake" class="mention hashtag" rel="tag">#<span>snakemake</span></a> 8.14 has been released. It supports setting the shell to use per rule if needed (e.g. if your analysis step runs in a container that does not have bash shell).<br /><a href="https://fosstodon.org/tags/sciworkflows" class="mention hashtag" rel="tag">#<span>sciworkflows</span></a> <a href="https://fosstodon.org/tags/reproducibility" class="mention hashtag" rel="tag">#<span>reproducibility</span></a><br /><a href="https://snakemake.github.io" target="_blank" rel="nofollow noopener" translate="no"><span class="invisible">https://</span><span class="">snakemake.github.io</span><span class="invisible"></span></a></p>
Common Workflow Language<p>Session 2 of the CWL Conference 2024 starts in an hour!</p><p>Program: <a href="https://www.commonwl.org/conferences/2024/#onlinesession2Schedule" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">commonwl.org/conferences/2024/</span><span class="invisible">#onlinesession2Schedule</span></a></p><p>You can still sign up for free; we give you the connection information automatically: <a href="https://forms.gle/1q2q7t5vVVjUhGKR7" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="">forms.gle/1q2q7t5vVVjUhGKR7</span><span class="invisible"></span></a></p><p>Can't attend Session 2, or did you miss Session 1? No worries, the videos are already online and linked from the program. Click through and you can also leave questions and comments for the presenters.</p><p><a href="https://floss.social/tags/CommonWL" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>CommonWL</span></a> <a href="https://floss.social/tags/SciWorkflows" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>SciWorkflows</span></a></p>
Johannes Köster<p><a href="https://fosstodon.org/tags/Snakemake" class="mention hashtag" rel="tag">#<span>Snakemake</span></a> has recently reached 1 million downloads on <a href="https://fosstodon.org/tags/Bioconda" class="mention hashtag" rel="tag">#<span>Bioconda</span></a>! <a href="https://snakemake.github.io" target="_blank" rel="nofollow noopener" translate="no"><span class="invisible">https://</span><span class="">snakemake.github.io</span><span class="invisible"></span></a><br /><a href="https://fosstodon.org/tags/sciworkflows" class="mention hashtag" rel="tag">#<span>sciworkflows</span></a> <a href="https://fosstodon.org/tags/reproducibility" class="mention hashtag" rel="tag">#<span>reproducibility</span></a></p>
Common Workflow Language<p>CWL v1.2.1 has been ratified and released!<br><a href="https://w3id.org/cwl/v1.2/" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="">w3id.org/cwl/v1.2/</span><span class="invisible"></span></a> </p><p>There are no new features nor behavior changes in CWL v1.2.1 as compared to CWL v1.2.0. </p><p>v1.2.1 fixes only typos, adds clarifications, and adds additional conformance tests.</p><p>Some changes to the schema defining CWL have been made to aid the auto-generation of libraries for the reading and writing of CWL documents.</p><p><a href="https://github.com/common-workflow-language/cwl-v1.2/releases/tag/v1.2.1" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/common-workflow-lan</span><span class="invisible">guage/cwl-v1.2/releases/tag/v1.2.1</span></a></p><p><a href="https://floss.social/tags/SciWorkflows" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>SciWorkflows</span></a> <a href="https://floss.social/tags/CommonWL" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>CommonWL</span></a></p>
Johannes Köster<p><a href="https://fosstodon.org/tags/snakemake" class="mention hashtag" rel="tag">#<span>snakemake</span></a> 7.21 has been released. It provides ergonomic improvements for parameter space exploration and reporting. Further, several corner case bugs have been fixed. Thanks a lot for all the awesome contributions! <a href="https://snakemake.github.io" target="_blank" rel="nofollow noopener" translate="no"><span class="invisible">https://</span><span class="">snakemake.github.io</span><span class="invisible"></span></a> <a href="https://fosstodon.org/tags/sciworkflows" class="mention hashtag" rel="tag">#<span>sciworkflows</span></a> <a href="https://fosstodon.org/tags/reproducibility" class="mention hashtag" rel="tag">#<span>reproducibility</span></a></p>
Samuel Lampa<p>(Seen on birdsite): Videos from the Workflows community summit 2022 posted online: <a href="https://www.youtube.com/playlist?list=PLAtmuqHExRvO-l-mACmlK_4mfmG6yLnpN" rel="nofollow noopener" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">youtube.com/playlist?list=PLAt</span><span class="invisible">muqHExRvO-l-mACmlK_4mfmG6yLnpN</span></a> <a href="https://genomic.social/tags/sciworkflows" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>sciworkflows</span></a></p>
Samuel Lampa<p>🎉 Hooray, after learning it is still used, I just pushed a new release of SciLuigi (wrapper around <span class="h-card"><a href="https://mstdn.social/@Spotify" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>Spotify</span></a></span> 's Luigi pipeline tool) tonight, for the first time in almost 3 years! 0.10.1 🎉 </p><p>Grab it while it's hot 👇 <br><a href="https://github.com/pharmbio/sciluigi#readme" rel="nofollow noopener" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/pharmbio/sciluigi#r</span><span class="invisible">eadme</span></a> <a href="https://genomic.social/tags/sciworkflows" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>sciworkflows</span></a></p>
Samuel Lampa<p>Current status: Updating the SciLuigi repo, after learning there are still some uses of it (which is cool!). Wish me luck! 🙂 <a href="https://github.com/pharmbio/sciluigi" rel="nofollow noopener" target="_blank"><span class="invisible">https://</span><span class="">github.com/pharmbio/sciluigi</span><span class="invisible"></span></a> <a href="https://genomic.social/tags/sciworkflows" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>sciworkflows</span></a></p>
Samuel Lampa<p>This was a good graphical explanation of <a href="https://genomic.social/tags/sciworkflows" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>sciworkflows</span></a> in general as well! (Can't believe so many people don't have a clue what they are 😅 ): </p><p><span class="h-card"><a href="https://octodon.social/@biocrusoe" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>biocrusoe</span></a></span> wrote:<br>&gt; The "Common Workflow Language" project explained in 64 seconds</p><p><a href="https://octodon.social/@biocrusoe/109465666896285618" rel="nofollow noopener" target="_blank"><span class="invisible">https://</span><span class="ellipsis">octodon.social/@biocrusoe/1094</span><span class="invisible">65666896285618</span></a></p>
Johannes Köster<p>So here is your first christmas present: <a href="https://fosstodon.org/tags/Snakemake" class="mention hashtag" rel="tag">#<span>Snakemake</span></a> 7.19 is released, adding native <a href="https://fosstodon.org/tags/SLURM" class="mention hashtag" rel="tag">#<span>SLURM</span></a> support, which <span class="h-card" translate="no"><a href="https://fediscience.org/@rupdecat" class="u-url mention">@<span>rupdecat</span></a></span> and I have implemented in the last months. Apart from that, the release provides various bug fixes. <a href="https://fosstodon.org/tags/sciworkflows" class="mention hashtag" rel="tag">#<span>sciworkflows</span></a> <a href="https://fosstodon.org/tags/reproducibility" class="mention hashtag" rel="tag">#<span>reproducibility</span></a> <a href="https://snakemake.github.io" target="_blank" rel="nofollow noopener" translate="no"><span class="invisible">https://</span><span class="">snakemake.github.io</span><span class="invisible"></span></a></p>
Johannes Köster<p><a href="https://fosstodon.org/tags/snakemake_wrappers" class="mention hashtag" rel="tag">#<span>snakemake_wrappers</span></a> 1.21.0 are released, with 15 updated wrappers, bugfixes for bcftools wrappers, and usability improvements for arriba and sambamba wrappers. <a href="https://snakemake-wrappers.readthedocs.io" target="_blank" rel="nofollow noopener" translate="no"><span class="invisible">https://</span><span class="ellipsis">snakemake-wrappers.readthedocs</span><span class="invisible">.io</span></a> <a href="https://github.com/snakemake/snakemake-wrappers/releases" target="_blank" rel="nofollow noopener" translate="no"><span class="invisible">https://</span><span class="ellipsis">github.com/snakemake/snakemake</span><span class="invisible">-wrappers/releases</span></a> <a href="https://fosstodon.org/tags/sciworkflows" class="mention hashtag" rel="tag">#<span>sciworkflows</span></a> <a href="https://fosstodon.org/tags/reproducibility" class="mention hashtag" rel="tag">#<span>reproducibility</span></a></p>
Johannes Köster<p><a href="https://fosstodon.org/tags/snakemake_wrappers" class="mention hashtag" rel="tag">#<span>snakemake_wrappers</span></a> 1.20.0 has been released with one new wrapper, 3 fixes, and 19 updated wrappers! <a href="https://github.com/snakemake/snakemake-wrappers/releases" target="_blank" rel="nofollow noopener" translate="no"><span class="invisible">https://</span><span class="ellipsis">github.com/snakemake/snakemake</span><span class="invisible">-wrappers/releases</span></a> <a href="https://snakemake-wrappers.readthedocs.io" target="_blank" rel="nofollow noopener" translate="no"><span class="invisible">https://</span><span class="ellipsis">snakemake-wrappers.readthedocs</span><span class="invisible">.io</span></a> <a href="https://fosstodon.org/tags/sciworkflows" class="mention hashtag" rel="tag">#<span>sciworkflows</span></a> <a href="https://fosstodon.org/tags/reproducibility" class="mention hashtag" rel="tag">#<span>reproducibility</span></a></p>
Johannes Köster<p>I am happy to announce <a href="https://fosstodon.org/tags/snakemake_wrappers" class="mention hashtag" rel="tag">#<span>snakemake_wrappers</span></a> 1.19.2. This time, 32 wrappers have been updated: <a href="https://github.com/snakemake/snakemake-wrappers/releases" target="_blank" rel="nofollow noopener" translate="no"><span class="invisible">https://</span><span class="ellipsis">github.com/snakemake/snakemake</span><span class="invisible">-wrappers/releases</span></a></p><p><a href="https://snakemake.readthedocs.io" target="_blank" rel="nofollow noopener" translate="no"><span class="invisible">https://</span><span class="">snakemake.readthedocs.io</span><span class="invisible"></span></a></p><p><a href="https://fosstodon.org/tags/sciworkflows" class="mention hashtag" rel="tag">#<span>sciworkflows</span></a> <a href="https://fosstodon.org/tags/reproducibility" class="mention hashtag" rel="tag">#<span>reproducibility</span></a> <a href="https://fosstodon.org/tags/snakemake" class="mention hashtag" rel="tag">#<span>snakemake</span></a></p>
Johannes Köster<p><a href="https://fosstodon.org/tags/Snakemake" class="mention hashtag" rel="tag">#<span>Snakemake</span></a> 7.18.2 is released. Most importantly, it fixes a bug occurring when inheriting multiple times from the same rule, and it provides more information about failing jobs. <a href="https://fosstodon.org/tags/sciworkflows" class="mention hashtag" rel="tag">#<span>sciworkflows</span></a> <a href="https://fosstodon.org/tags/reproducibility" class="mention hashtag" rel="tag">#<span>reproducibility</span></a> <a href="https://snakemake.github.io" target="_blank" rel="nofollow noopener" translate="no"><span class="invisible">https://</span><span class="">snakemake.github.io</span><span class="invisible"></span></a></p>
Johannes Köster<p><a href="https://fosstodon.org/tags/snakemake_wrappers" class="mention hashtag" rel="tag">#<span>snakemake_wrappers</span></a> 1.19.1 are released, with 90 updated wrappers. <a href="https://snakemake-wrappers.readthedocs.io" target="_blank" rel="nofollow noopener" translate="no"><span class="invisible">https://</span><span class="ellipsis">snakemake-wrappers.readthedocs</span><span class="invisible">.io</span></a> <a href="https://fosstodon.org/tags/sciworkflows" class="mention hashtag" rel="tag">#<span>sciworkflows</span></a> <a href="https://fosstodon.org/tags/reproducibility" class="mention hashtag" rel="tag">#<span>reproducibility</span></a> <a href="https://fosstodon.org/tags/modularization" class="mention hashtag" rel="tag">#<span>modularization</span></a></p>
Daniel S. Katz<p>The Workflows Community Initiative&#39;s November 2022 newsletter has been published: <br /><a href="https://mailchi.mp/919b5d9fe842/wci-newsletter-october-9288215" target="_blank" rel="nofollow noopener" translate="no"><span class="invisible">https://</span><span class="ellipsis">mailchi.mp/919b5d9fe842/wci-ne</span><span class="invisible">wsletter-october-9288215</span></a></p><p>Register for the Workflows Community Summit (Nov 29 and 30, 2022) and join the Workflows Community BoF at SC22 on Nov 15.</p><p><a href="https://fosstodon.org/tags/hpc" class="mention hashtag" rel="tag">#<span>hpc</span></a> <a href="https://fosstodon.org/tags/workflow" class="mention hashtag" rel="tag">#<span>workflow</span></a> <a href="https://fosstodon.org/tags/SciWorkflows" class="mention hashtag" rel="tag">#<span>SciWorkflows</span></a></p>