Nextclade version bump

[marcmtk]

Hi there! I've only just discovered nf-core and this pipeline, i'm very impressed with how polished it is.

Is your feature request related to a problem? Please describe

I noticed that nextclade is quite out of date, this leads to wrong clade calls. Currently the javascript implementation version 0.14.4 is used, the newest version is 1.3.0 (updated today).

Describe the solution you'd like

I'd like to see the version of nextclade increased. From what i can tell the newest version widely disseminated is 1.2.3
Conda: bioconda::nextclade=1.2.3
Singularity: https://depot.galaxyproject.org/singularity/nextclade:1.2.3--h9ee0642_0
Biocontainer: quay.io/biocontainers/nextclade:1.2.3--h2eeb373_1

Describe alternatives you've considered

I've considered trying to bump the version myself, but i'm unsure how the code should be distributed between this repository and nf-core/modules. Also i'm very new to nextflow, so it's a bit overwhelming 😄

Additional context

Nextclade has received new required input parameters and removed at least one used output-parameter

Added required input for v. 1.2.3

• --input-root-seq should match the genome parameter
• --input-tree Path to Auspice JSON v2 file containing reference tree.
• --input-qc-config Path to a JSON file containing configuration of Quality Control rules

Removed output option

• --output-tsv-clades-only which i think is used downstream in the multiQC

Also it appears that the next version of nextclade (1.3.0) introduces a simpler input specification --input-dataset=data/sars-cov-2

[drpatelh]

Added in #254

See website docs for usage information.

To summarise:

A nextclade dataset feature was introduced in Nextclade CLI v1.3.0 that fetches input genome files such as reference sequences and trees from a central dataset repository. We have uploaded Nextclade dataset v2022-01-05 to nf-core/test-datasets, and for reproducibility, this will be used by default if you specifiy --genome 'MN908947.3' when running the pipeline. However, there are a number of ways you can use a more recent version of the dataset:

• Supply your own by setting: --nextclade_dataset <PATH_TO_DATASET>
• Let the pipeline create and use the latest version by setting: --nextclade_dataset false --nextclade_dataset_tag false
• Let the pipeline create and use a specific, tagged version by setting: --nextclade_dataset false --nextclade_dataset_tag <DATASET_TAG>

If the --save_reference parameter is provided then the Nextclade dataset generated by the pipeline will also be saved in the results/genome/ directory.