Argument input-fasta is missing in NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:CONSENSUS_QC:NEXTCLADE_RUN" about viralrecon HOT 4 OPEN

I do see now in the genome folder that the Nextclade version that it downloaded is this one: nextclade_sars-cov-2_MN908947_2022-06-14T12_00_00Z
so that is the one that it is using.

How can I make it use the most recent one? I thought that adding it to the command line, it would overwrite the version from the module.

from viralrecon.

Actually I went in the modules and added -i before $fasta in the main.nf files that are in the nextclade folder. That one was fixed and I got a different error: Error: at least one of output path arguments required: --output-json, --output-csv, --output-tsv-clades-only, --output-tsv, --output-tree
So I will try to do the same for these and report back.

from viralrecon.

I added output lines in the main.nf from nextclade/run folder. Could you correct them because I am not sure I am using $prefix correctly. This is how that section is looking now:
nextclade \
run \
$args \
--jobs $task.cpus \
--input-dataset $dataset \
--output-all ./ \
--output-json ./${prefix} \
--output-csv ./${prefix} \
--output-tsv ./${prefix} \
--output-tsv-clades-only ./${prefix} \
--output-tree ./${prefix} \
--output-all ./${prefix} \
--output-basename ${prefix} \
-i $fasta

from viralrecon.

Hi @CeliaRodrigues ! It's weird because for us is enough with this code to work:

nextclade \
    run \
     \
    --jobs 2 \
    --input-dataset nextclade_sars-cov-2_MN908947_2024-05-08--11-39-52Z \
    --output-all ./ \
    --output-basename SAMPLE3_SE \
    SAMPLE3_SE.consensus.fa

It does not seem to need all those params you're showing. Might it be related to the nextclade version? Which version are you using?

We use these to make nextclade always run in the latest version for SARS-CoV-2:

params.yml

nextclade_dataset_name: 'sars-cov-2'
nextclade_dataset: false
nextclade_dataset_tag: '2024-05-08--11-39-52Z'

custom.config:

withName: 'NEXTCLADE_DATASETGET|NEXTCLADE_RUN' {
container = 'https://depot.galaxyproject.org/singularity/nextclade:3.4.0--h9ee0642_0'
}

Are you using latest nextflow version and latest nextclade version? Let me know if you manage to solve the problem please 😄

from viralrecon.