M Bernt

Advanced workflow tips/tricks FAQ / mini tutorial

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Lets start with an idea collection that we may turn into FAQ list or mini tutorial: - Run a tool based on the presence or absence of an optional input....

Link dada2 and qiime2 tutorials

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- dada2: https://benjjneb.github.io/dada2/tutorial.html The tutorial is for R, but since the Galaxy tools wrap the R functions 1:1 it should be easy to follow. - qiime2: https://docs.qiime2.org/jupyterbooks/cancer-microbiome-intervention-tutorial/index.html (for the steps...

Mothur tutorial still has wrong sample number / misses a sample

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> thanks. how did I not catch this sooner :P Actually it seems to be 9 early samples + 10 late samples (+ 1 batch) since for some reason F3D4...

Hi there, The Galaxy community maintains tool wrapper for [dada2](https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2) since quite some time and since recently also a [workflow](https://github.com/galaxyproject/iwc/tree/main/workflows/amplicon/dada2). Clearly a tutorial could increase visibility even more, e.g. in...

Small (mock) reference data

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For the [Galaxy tool](https://github.com/galaxyproject/tools-iuc/blob/main/tools/gtdbtk/gtdbtk_classify_wf.xml) the classify workflow it would be great if there would be small reference data to run a test in the CI. Is there a possibility to...

and skip more linters (we only want the biocontainers check here) 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...

dada2 use default_identifier_source

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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)...

Mothur 1.48

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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...

Fixes: https://github.com/galaxyproject/tools-iuc/issues/5709 https://github.com/galaxyproject/tools-iuc/issues/65 Started ... - [ ] include https://github.com/galaxyproject/tools-iuc/pull/4347 and https://github.com/galaxyproject/tools-iuc/pull/4734 - [ ] check https://github.com/galaxyproject/tools-iuc/issues/4009 https://github.com/galaxyproject/tools-iuc/issues/4100 https://github.com/galaxyproject/tools-iuc/issues/4085 https://github.com/galaxyproject/tools-iuc/issues/4095 https://github.com/galaxyproject/tools-iuc/issues/4091 - [ ] all tools need tests - [...

I just discovered that the emboss tools have a binary that generates Galaxy tool wrappers (and it seems that the original ones have been generated this way .. but this...