RE: https://mas.to/@nanopub/116714551434180700

One talk will be from me about #Snakemake and creating #nanopub reports. See you!

Just discovered that the new "Paper I have read" #nanopub template has a label field. This will be quite a motivation for me to register more for some time to SparQL in the future.

Could not resist registering the #OSPARK output by @saranjeet and others about "Managing Outreach on Open Research Material to Heterogeneous Groups": https://w3id.org/np/RAxi5mJwS-F0iSUJ73x_mL_WPMo3piv5FX44Ll9t2Bnu4

Nice read!

RE: https://mas.to/@nanopub/116619026431272841

A presentation about #Snakemake and software provenance with #nanopub by Yours Truthfully.

Of interest for those in the Snakemake workflow management system and citing workflow metadata in academic journals. Related to https://fediscience.org/@snakemake/116523521544819091 - oh, and I just realized a typo in the announcement bot message 😉

Today:

- written a blurb for my presentation at the upcoming #nanopub session
- release the #SLURM executor plugin for #Snakemake v2.7.0 - see https://fediscience.org/@snakemake/116617420491776431
- tried to mitigate the issue that TMOUT on an HPC login brings: sending SIGHUB to all detached multiplexers (so far no remedy and I tried a lot(!), don't send me tips).
- futile further debugging attempts. In the end it worked. Might result in a new release next week.

#academicchatter

Just published a nanopublication to list all other nanopubs mentioning the Snakemake Workflow Management System: https://w3id.org/np/RAzeQbv1gXqKIuLic4xTP1gYRnL4YhU_5oRl62nbNl2Xk

Not yet sophisticated, but I am starting to like #SparQl 😉

#nanopub #Snakemake

RE: https://fediscience.org/@snakemake/116523521544819091

Software provenance with #Snakemake: Using the reporter plugin for nanopublications, we can now get slightly improved nanopublications like this one: https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g (press on the little blue arrow on the right to see the full details). Automatically captured for this workflow: https://w3id.org/np/RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE - again expressed a nanopub declaration. 😉

It now supports to capture the "classic" software support for #Conda and Snakemake wrappers.

There is more work to do. Let's see when and if I get to it.

#reproducibleComputing #softwareprovenance #nanopub

RE: https://fediscience.org/@snakemake/116443839004108636

Now, folks, this is my first release of a Snakemake reporter plugin!

I am pretty proud of it, but it would have been impossible without the input of @johanneskoester , @tkuhn and - most of all - @fbartusch !

What is it about?

Have you ever read a #bioinformatics paper and thought: "Hugh? How did they get there? This is absolutely not #reproducibleComputing , because I cannot apply it!"

The Snakemake Workflow Management System helps researchers by generating a self-contained HTML report with all bells and whistles (all software metadata, runtime stats and publication-ready figures). And yet, I felt it is time to easy writing the materials & methods section.

Declare a worfklow #nanopub using this template: https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk and get a declaration like this: https://w3id.org/np/RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE

Use this reporter plugin and get all metadata reference in one other nano publication: https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE

1/3