MarieLataretu

initial commit for subwf fastq_extract_kraken_krakentools

2

## 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

3

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

1

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

5

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

1

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

7

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...