MarieLataretu

initial commit for subwf fastq_extract_kraken_krakentools

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## PR checklist Closes #5241 - [x] This comment contains a description of changes (with reason). - [x] If you've fixed a bug or added code that should be tested,...

### Is there an existing subworkflow for this? - [X] I have searched for the existing subworkflow ### Is there an open PR for this? - [X] I have searched...

Bug/question with --force-all-parents --clades all

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Hi there, I just was wondering why I have no output and tried the second example from here: https://github.com/lenaschimmel/sc2rf#no-output--some-sequences-not-shown So I added `--clades all --force-all-parent` to my call, but it...

Update medaka to get the latest models

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The latest Medaka version [v.1.11.3.](https://github.com/nanoporetech/medaka/releases/tag/v1.11.3) comes with updated models, `r1041_e82_400bps_*_v4.3.0`, which matches the latest MinKNOW version. Currently, we have an ARTIC container with Medaka version 1.8.0. I'll try to create...

Catch identical filenames

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I suggest to change `simpleName` to `baseName` here: https://github.com/replikation/poreCov/blob/9ba98fe38d666508fa7dd0bd16d4accc5fe36a4b/poreCov.nf#L183 (and potentially somewhere else) to avoid problems with file names with more than one `.`. Else or in addition a sanity...

Private mutation from nextclade

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Private mutation from the nextclade output can help to detect recombinants, mixed infections or contamination, [see Twitter](https://twitter.com/nextstrain/status/1485730636564414469) We could add the following columns to the datatable: `"privateNucMutations.reversionSubstitutions", "privateNucMutations.labeledSubstitutions", "privateNucMutations.unlabeledSubstitutions", "qc.privateMutations.status"`...

**Is your feature request related to a problem? Please describe.** I wanted to look at the mappings and selected the "wrong" reference file `NC_045512.2.fasta` from the [`/data/reference_nCov19/`](https://github.com/replikation/poreCov/tree/master/data/reference_nCov19) folder. **Describe the...

LILO with SLURM

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Hi there, I'm trying to run LILO on a SLURM HPC and I'm not sure what the errors are related to. Do you have an idea? It seems really environment...

After some time of confusion as to why the snapshot file was _not_ generated, while the test passed, I discovered that I was missing the `match()` function: ``` then {...

Hi there, I try to activate multiple local jar plugins (nf-test 0.8.4): ``` nf-test test my-test.nf.test --plugins path/to/my/nft-plugin.jar,path/to/my/nft-plugin2.jar ``` However, the list is not split: ``` Plugin 'path/to/my/nft-plugin.jar,path/to/my/nft-plugin2.jar' not found....