Dan Fornika

New module: Bracken

7

- [x] This comment contains a description of changes (with reason) - [x] `CHANGELOG.md` has been updated - [x] There is example tool output for tools in the https://github.com/ewels/MultiQC_TestData repository...

Bracken Data Manager: Add support for pre-built DBs

3

Issue #4073 describes the need to update the links that the Kraken2 data manager uses to pull the pre-built 'MiniKraken2' database. The 'canonical' place to find that database is now...

We've been using [dragonflye](https://github.com/rpetit3/dragonflye) for some hybrid assemblies recently and have noticed a few unexpected results when running mob-recon on the assemblies. In one example, mob-recon included a small (~2kb)...

No '-main' function in dev_server

1

I get the following error & stacktrace (I've truncated it for brevity) when I do `lein run` on the ``` Exception in thread "main" java.lang.Exception: Cannot find anything to run...

Would it simplify the testing setup to drop galaxy-bootstrap and use the galaxy-stable docker image to test against? See: https://github.com/dfornika/clj-blend/blob/master/.travis.yml

Retry on failure?

2

I'm working on a [galaxy wrapper](https://github.com/galaxyproject/tools-iuc/pull/2671) for this tool. During my testing of the tool wrapper, I've noticed that downloads will sometimes fail. I'd like to have a way to...

KeyError in `format_pileup.py`

3

We've seen an error in `format_pileup.py` where a `KeyError` can be triggered here: https://github.com/jts/ncov-tools/blob/7a19778c644594fe17ce4fc703560e97b149aa60/workflow/scripts/format_pileup.py#L23 ``` Traceback (most recent call last): File "ncov-tools/workflow/rules/../scripts/format_pileup.py", line 23, in freqs[b] += 1 KeyError: 'N'...

Plotting scripts may crash if no metadata (Ct values) available

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We have an automated system that pulls metadata (collection dates and Ct values) for all samples prior to running artic & ncov-tools. We've recently run into a situation where no...

Proposed fix for #108 There may be other ways to handle this but here's one option. If the merged dataframe is empty, write an empty plot (so the snakemake pipeline...

Integrate into a 'Galaxy Interactive Environment'

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## Description This is a suggestion for a Mozilla Global Sprint 2018 activity. It would be great to be able to install PhyloProfile as a [Galaxy Interactive Environment](https://docs.galaxyproject.org/en/master/admin/interactive_environments.html). That might...