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Hey,
When I try to run the [demo using Snakemake rules,](https://github.com/wir963/HATCHet-demo) I get two errors.
The first error is for `count_alleles` and it basically complains that the ph…
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Hello,
I am trying to run Reago v.1.1 on a set of metagenomes. But the "filter_input" step aborts after identifying only two 16S reads ( I know there are lots more from using Emirge and from prelimina…
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Currently, WES supports standard keywords for `CWL` and `WDL` workflow languages. Can we add a new `workflow_type` keyword supporting Nextflow-based workflows, perhaps `NEXTFLOW`?
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The big question is how to organize rules/workflows.
My pipeline had the hierarchy:
> # snakefile
>
> Contain sample name and basic organization
> imports workflows
> ## workflow
>
> contains proc…
jfear updated
8 years ago
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Hi,
Thank you for providing Snakemake. Here is my bug report:
**Snakemake version**
Any version from 7.3.3 onwards.
**Describe the bug**
I'm using Snakemake on a cluster with a SLURM cookie…
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What would be the best practices for doing modern reproducable (and scalable?) science?
- Jupyter notebooks?
- github/gitlab repos?
- published FAIR datasets?
- ???
issues:
- on cloud / …
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Hi,
We have installed Agnostos-wf and in our first attempt to analyze our metagenomic data we got the error bellow (in bold) after running 'db_creation' workflow
Used command line:
_snakem…
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If a repository is forked from another source, its issues will be disabled by default.
If I then report an issue with the profile to the original source, this will not be automatically propagated t…
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- switch modules to containers (#42)
- remove any biowulf-specific code from driver script
- remove hard-coded biowulf paths from config, or document them well
- test on FRCE to verify that it work…
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Problem:
I would like to use the command line to alter a single command of the config file. This feature is nicely implemented for simple parameters (e.g., config['simple']), but is cumbersome for ne…