Open CeliaRodrigues opened 8 months ago
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.
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.
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
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 😄
Description of the bug
The pipeline was running correctly until it had to retrieve a consensus fasta file with Nextclade. The parameter seems to be missing and I do not know how to add it when running a Singularity image. I did install Nextclade with conda and I am calling the most recent version I could find in my input command. I can see the fasta file the pipeline is calling in the folders so that is not the issue, I would need to have --input-fasta or -i added before the file.
Command used and terminal output
Relevant files
No response
System information
Nextflow version 23.04.4.5881 Container: Singularity 4.0.0 nf-core version 2.10 nf-core/viralrecon: Downloaded the master with nf-core download so it should be this latest release Environment was created with miniconda I am running it in Mobaxterm installed in a windows computer and I have the ubuntu wsl2 running.