Hi folks, I am attempting to run the ampliseq pipeline but I am running into the following errors: At the very top of the output log, I see this warning

N E X T F L O W  ~ version 25.10.0

WARN: Missing params file variable: ${nfcore_output}
WARN: Missing params file variable: ${nfcore_output}

Then the pipeline exits with the following errors:

Use DADA2 taxonomy classification
ERROR ~ No such file or directory: /temp180/mpfrende/nvincen2/Metagenomics/nf-core_ampliseq/nfcore_scripts/${nfcore_output}/assets/report_template.Rmd

 -- Check '.nextflow.log' file for details
ERROR ~ No such file or directory: /temp180/mpfrende/nvincen2/Metagenomics/nf-core_ampliseq/nfcore_scripts/${nfcore_output}/assets/nf-core_style.css

The nextflow call is as follows:

nextflow run nf-core/ampliseq \
-profile apptainer \
-params-file ampliseq-nf-params.yml

In the params file I have specified an output directory with

outdir: /temp180/mpfrende/nvincen2/Metagenomics/nf-core_ampliseq/nfcore_output

No idea. Nextflow seems to be looking for pipeline code. Try

nextflow pull nf-core/ampliseq -r 2.15.0

to make sure the pipeline is downloaded

Yes, I tried that, and also going back to an earlier version in 2.14.0, but kept getting the same error. Is there any other information I can provide to help troubleshoot?

You will need to specify some input, see https://nf-co.re/ampliseq/2.15.0/docs/usage/#input-specifications. You might want to start reading with https://nf-co.re/ampliseq/2.15.0/docs/usage/#quick-start though. If thats indeed the problem, then the error message seems unhelpful and will need improvement. So please let us know how it goes.

I realized the problem - I was using a weird format when specifying the output report files in the params file. I fixed that and this error stopped. However, I am now running into different errors that are halting the pipeline at different steps. I will start a new thread about those errors since they appear unrelated to this one. Thank you for your help!