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miniwdl allows any of its configuration options to be overridden by environment variables ([details](https://miniwdl.readthedocs.io/en/latest/runner_reference.html?highlight=errata#configuration)). Th…
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There is a [fork of this lesson in the Carpentries Incubator](https://github.com/carpentries-incubator/workflows-snakemake) which focusses purely on Snakemake (and that is indeed the majority of the c…
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When I try to build (`showyourwork`, `showyourwork build`) using showyourwork v0.4.2 I get the following error:
```
(syw) [krosenfeld@internal.idm.ctr@ipapvwks25 pysr_paper]$ showyourwork build …
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When providing Illumina and Nanopore reads, the pipeline fails at `rule circularize_final` because there is no directory called `{sample}/3.circularization/3.circular_sequences/sh`, which should have …
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There are existing resources that we can point to as starting point:
- [Alli's Epi Handbook](https://alliblk.github.io/genepi-book/)
- [Nextstrain VEME tutorial](https://github.com/blab/veme-2022) …
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My workflow has rules that contain `conda:` environment specifications.
The file that is pointed to never existed and this was never a problem.
Now suddenly I get an error when a rule that conta…
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We should make a docker env for our pipeline (or for each workflow) and run in those instead
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as the dataset_description and the README.md are required by the specification
https://bids-specification.readthedocs.io/en/latest/modality-agnostic-files.html
I think there should be a way to a…
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I attempted to reproduce your data, but encountered the following error. Could you please assist me in resolving this issue?
[Wed Oct 9 04:38:59 2024]
Error in rule refine:
jobid: 447
inp…
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I'm having an issue when running STAR. I'm running it in a snakemake workflow.
It's weird because it was previously working. This is the issue:
EXITING because of FATAL ERROR: number of bytes ex…