Bug report

We are starting to add container specific configs to nf-core, see the seqera-containers-conversion-manual branch of the testpipeline as an example. We thought we could use nextflow inspect -profile singularity to easily pull all singularity containers specified in conf/containers_singularity_linux_amd64.config for nf-core pipelines download but this is not the case.

Expected behavior and actual behavior

nextflow inspect -profile singularity should print the containers from the singularity profile which are in conf/containers_singularity_linux_amd64.config

Instead we get the containers as specified in the main.nf of the modules themselves, e.g. https://github.com/nf-core/testpipeline/blob/seqera-containers-conversion-manual/modules/nf-core/fastqc/main.nf#L6

Steps to reproduce the problem

run nextflow inspect -profile singularity . inside the seqera-containers-conversion-manual branch of the testpipeline

Program output

nextflow inspect . -profile singularity
{
    "processes": [
        {
            "name": "FASTQC",
            "container": "fastqc:0.12.1--af7a5314d5015c29"
        },
        {
            "name": "MULTIQC",
            "container": "multiqc:1.32--d58f60e4deb769bf"
        }
    ]
}

Environment

• Nextflow version: 25.10.2
• Java version: Groovy 4.0.28 on OpenJDK 64-Bit Server VM 17.0.6+10
• Operating system: macOS 26.2
• Bash version: zsh 5.9 (arm64-apple-darwin25.0)