Patrik Smeds

fix: handle benmark bug that arise with singularity

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### Description Running snakemake with singularity results in (nearly) empty benchmark statistics. benchmark tries to read a process with name "starter-suid" which raise a AccessDenied event, resulting in that the...

test: test to evaluate pipelines that using modules that them self use modules.

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Tests used to import a module that contain a module, see issue #1626 ### QC * [x] The PR contains a test case for the changes or the changes are...

feat: add gitfile option to make it possible to use local git repos when importing modules

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Feat: add gitfile option to make it possible to use local git repos when importing modules. Should make it possible to include module like this: ``` module dna_seq: snakefile: gitfile("file:///beegfs-storage/LOCAL_PATH/dna-seq-gatk-variant-calling",...

feat: genefuse wrapper

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### Description Wrapper used to run genefuse ### QC For all wrappers added by this PR, I made sure that * [x] there is a test case which covers any...

Unable to use LocalGitFile

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https://github.com/snakemake/snakemake/blob/1349254de57ced0466bfe1e98f0f7c2a1b247d2d/snakemake/sourcecache.py#L328-L353 I have successfully been using sourcecache.GithubFile to be able to import snakemake module located on github but not been able to use GitLocalFile to import local repos, which is...

It would be really useful if one could set which snakemake version that should be used. Our workflows started to fail when a new version of snakemake was released.

Interactive BlobToolKit: not displaying output

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### Describe the bug Pull-request [18630](https://github.com/galaxyproject/galaxy/pull/18630) adds Interactive BlobToolkit to the list of interactive tools. The tool is visible, will run successfully but not display any output. **Tool Standard Output**...

we plan to add kmindex (https://github.com/tlemane/kmindex ) to tools-iuc. As the tool uses a unique index format, a dedicated Galaxy datatype will be introduced to support it. (Please replace this...

Add kmindex

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FOR CONTRIBUTOR: * [ ] I have read the [CONTRIBUTING.md](https://github.com/galaxyproject/tools-iuc/blob/master/CONTRIBUTING.md) document and this tool is appropriate for the tools-iuc repo. * [ ] License permits unrestricted use (educational + commercial)...

found incorrect/missing assembly_link_type

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Hi! I have been playing around with python and the api library generated from (https://www.ncbi.nlm.nih.gov/datasets/docs/v2/openapi3/openapi3.docs.yaml) and found a missing data typ or incorrect set data value when trying to get...