"Schema.org for research data managers: a primer"; has a nice section on #SciWorkflows

Article abstract: https://www.inderscience.com/info/inarticle.php?artid=128449

DOI (direct to PDF!): https://doi.org/10.1504/IJBDM.2022.10048569

#SciWorkflows

https://w3id.org/cwl/view/git/03b8da4ede3afcbf97b4e780c153155f33e76c84/pipeline.cwl

from

"A Unified Pipeline for FISH Spatial Transcriptomics" Cecilia Cisar, Nicholas Keener, Mathew Ruffalo, Benedict Paten bioRxiv 2023.02.17.529010; doi: https://doi.org/10.1101/2023.02.17.529010

Check out the confirmed talks for the CWL 2023 Conference! https://cwl.discourse.group/t/schedule-of-confirmed-talks/753

You can still sign up to participate: https://survey.bio-it.embl.de/614492

#CommonWL #SciWorkflows

#snakemake 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! https://snakemake.github.io #sciworkflows #reproducibility

If you can come to Heidelberg, Germany, then please consider attending one or both of these in-person CWL events hosted by EMBL and sponsored by ELIXIR-DE/de.NBI:

1. Tuesday, February 28th there will be an in-person CWL training & BYOW (Bring Your Own Workflow) co-working time
2. Wednesday, March 1st, we will participate in Session 2 of the CWL conference in-person, followed by lunch and then in participant-organized breakout sessions

https://bio-it.embl.de/events/cwlcon-2023-heidelberg/

#SciWorkflows #deNBI #Bioinformatics #ELIXIRDE

The 2023 Common Workflow Language conference is coming, and there is still time to submit your talk proposals!

https://cwl.discourse.group/t/deadline-for-talk-proposals-is-monday-january-16th-2023/720 #CommonWL #SciWorkflows

Toil 5.8.0 is out!

Highlights include "exposing workflow tasks via WES"
https://github.com/DataBiosphere/toil/releases/tag/releases%2F5.8.0

Also for toil-cwl-runner: --no-compute-checksum, --strict-cpu-limit, --disable-validate, and --fast-parser are now supported; along with the proposed CUDARequirement extension

#SciWorkflows #CommonWL

(Seen on birdsite): Videos from the Workflows community summit 2022 posted online: https://www.youtube.com/playlist?list=PLAtmuqHExRvO-l-mACmlK_4mfmG6yLnpN #sciworkflows

🎉 Hooray, after learning it is still used, I just pushed a new release of SciLuigi (wrapper around @Spotify 's Luigi pipeline tool) tonight, for the first time in almost 3 years! 0.10.1 🎉

Grab it while it's hot 👇
https://github.com/pharmbio/sciluigi#readme #sciworkflows

Current status: Updating the SciLuigi repo, after learning there are still some uses of it (which is cool!). Wish me luck! 🙂 https://github.com/pharmbio/sciluigi #sciworkflows

This was a good graphical explanation of #sciworkflows in general as well! (Can't believe so many people don't have a clue what they are 😅 ): https://octodon.social/@biocrusoe/109465666896285618

So here is your first christmas present: #Snakemake 7.19 is released, adding native #SLURM support, which @rupdecat and I have implemented in the last months. Apart from that, the release provides various bug fixes. #sciworkflows #reproducibility https://snakemake.github.io

RT @johanneskoester
#snakemake_wrappers 1.21.0 are released, with 15 updated wrappers, bugfixes for bcftools wrappers, and usability improvements for arriba and sambamba wrappers. https://snakemake-wrappers.readthedocs.io https://github.com/snakemake/snakemake-wrappers/releases #sciworkflows #reproducibility

#snakemake_wrappers 1.21.0 are released, with 15 updated wrappers, bugfixes for bcftools wrappers, and usability improvements for arriba and sambamba wrappers. https://snakemake-wrappers.readthedocs.io https://github.com/snakemake/snakemake-wrappers/releases #sciworkflows #reproducibility

The "Common Workflow Language" project explained in 64 seconds

#CommonWL #SciWorkflows

#snakemake_wrappers 1.20.0 has been released with one new wrapper, 3 fixes, and 19 updated wrappers! https://github.com/snakemake/snakemake-wrappers/releases https://snakemake-wrappers.readthedocs.io #sciworkflows #reproducibility

I am happy to announce #snakemake_wrappers 1.19.2. This time, 32 wrappers have been updated: https://github.com/snakemake/snakemake-wrappers/releases

https://snakemake.readthedocs.io

#sciworkflows #reproducibility #snakemake

#Snakemake 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. #sciworkflows #reproducibility https://snakemake.github.io

#snakemake_wrappers 1.19.1 are released, with 90 updated wrappers. https://snakemake-wrappers.readthedocs.io #sciworkflows #reproducibility #modularization

The Workflows Community Initiative's November 2022 newsletter has been published:
https://mailchi.mp/919b5d9fe842/wci-newsletter-october-9288215

Register for the Workflows Community Summit (Nov 29 and 30, 2022) and join the Workflows Community BoF at SC22 on Nov 15.

#hpc #workflow #SciWorkflows