Downloaded Singularity images don't match Apptainer

[JosuaCarl]

Description of the bug

When trying to pre-fetch container images for offline runs via nf-core pipelines download, the fetched Singularity images don't always correspond to the Apptainer images.

The error I get is:

command: apptainer pull  --name community.wave.seqera.io-library-multiqc-1.33--ee7739d47738383b.img.pulling.1782396783570 docker://community.wave.seqera.io/library/multiqc:1.33--ee7739d47738383b > /dev/null
  status : 255
  hint   : Try and increase apptainer.pullTimeout in the config (current is "20m")
  message:
    INFO:    Converting OCI blobs to SIF format
    INFO:    Starting build...
    INFO:    Fetching OCI image...
    INFO:    Extracting OCI image...
    FATAL:   While making image from oci registry: error fetching image to cache: while building SIF from layers: packer failed to pack: while unpacking rootfs: while unpacking layer sha256:8840f84a155a90fa826cbc2860acb0b176f13fa43bd2f0bc1d86e1e2c8218776: unpack entry: opt/conda/pkgs/python-3.14.2-h32b2ec7_100_cp314/lib/libpython3.14.so.1.0: unpack to regular file: short write: write /tmp/build-temp-2843846969/rootfs/opt/conda/pkgs/python-3.14.2-h32b2ec7_100_cp314/lib/libpython3.14.so.1.0: no space left on device

This is not surprising, because nextflow inspect -format json -profile apptainer,test,test_full nf-core/demo -r 1.1.0produces:

{
    "processes": [
        ...
        {
            "name": "MULTIQC",
            "container": "community.wave.seqera.io/library/multiqc:1.33--ee7739d47738383b"
        },
        ...
    ]
}

and nextflow inspect -format json -profile singularity,test,test_full nf-core/demo -r 1.1.0 returns:

        {
            "name": "MULTIQC",
            "container": "https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/34/34e733a9ae16a27e80fe00f863ea1479c96416017f24a907996126283e7ecd4d/data"
        },

Therefore the right container is not fetched.

Command used and terminal output

nf-core pipelines download nf-core/demo \
    -r 1.1.0 \
    --outdir test \
    --container-system singularity \
    --container-cache-utilisation copy \
    --download-configuration yes \
    --compress none

System information

Nextflow version (eg. 26.04.4)
OS (Linux & macOS)
Version of nf-core/tools (eg. 1.10, 1.12.1, 1.13)
Python version 3.12