Using the latest code on dev (ab8ca2e)

• Run nf-core create and customise the template to NOT include nf-core/configs
• Run nextflow run . -profile test,docker --outdir ./results in the newly created pipeline
• The warning below will be generated:

$ nextflow run . -profile test,docker --outdir ./results                     
N E X T F L O W  ~  version 23.04.1
Launching `./main.nf` [cheesy_bartik] DSL2 - revision: f334315f42
WARN: The following invalid input values have been detected:

* --config_profile_name: Test profile
* --config_profile_description: Minimal test dataset to check pipeline function
* --fasta: https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.fna.gz

This is because the following parameters are excluded from the template if nf-core/configs aren'part of the template:

The warning is being generated for --fasta because I also chose to exclude igenomes from the template which means this isn't there:

We need to change that block to include these parameters because they are still used in the test configs.