poreCov

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Freyja integration

1

Integration of Freyja for metagenomic screening of reads. Includes also a restructuring of the LCS-tool for metagenomic read-analysis.

DataSpott

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...

MarieLataretu

Publish VCF files

1

For many downstream analysis it would be nice to also publish the VCF files with the ref/alternate allele and the frequencies.

hoelzer

update guppy

4

new guppy version 6 does not require arrangement files for demultiplexing and has some changes demulti like this ``` process collect_fastq { label 'demultiplex' input: tuple val(name), val(technology), path(dir) output:...

replikation

Idea for the report table: A mini-plot that shows where Ns are in the assemblies

14

Could also include warnings when N stretches are in important regions, e.g. the spike protein As any mutations/deletions/insertions are just omitted when the corresponding region isn't covered enough, this might...

RaverJay

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...

MarieLataretu

Include artic-tools "validate_scheme"

1

Custom Primer bed-files can be tricky to set up the right way, so that Medaka will recognize them. In case of an error with the bed-file the medaka-process just fails...

DataSpott

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"`...

MarieLataretu

It happens quite frequently that FSs are introduced in consensus sequences. In almost all cases these are errors. Suggestion: We could integrate a new tool `proovframe` to correct FS based...

hoelzer

**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...

MarieLataretu