eliminating Apptainer cache duplication

[tmoughamer]

It seems that when using the Apptainer profile container images get stored by both Nextflow's (such as defined with NXF_SINGULARITY_CACHEDIR) and under the user's ~/.apptainer. For example, running nf-core's ATACseq. I get 26 pairs of files with the same hash. With each set amounting to 3.5G which is not insignificant. Is there a good way to keep this to one copy? I've triad to invoke apptainer's --disable-cache that has not worked. Setting $APPTAINER_CACHEDIR to /dev/null seemed another but might not be desired outside of use with Nextflow.

I'm running Nextflow version 23.10.0 build 5889.

nextflow run nf-core/atacseq -profile test,singularity --outdir ./atacseq_out

Here I show md5sum of files from each directory (I now know .apptainer files are named by their sha256).

$ cut -d' ' -f1 nxf_apptainer_cache.md5 apptainer_cache_net.md5 | sort | uniq -c
      2 1926bfa97ad83817aa533bef47fa70f5
      2 1bcf7a45e27bcf0a91819ccbeb236c71
      2 244ee7bd7063cc3684514a09ab39338a
      2 2acb7b16cebc8be79c7ca96780d01f99
      2 3127b43ba30b44be760c1d03c2e28288
      2 32ef376bdbbd22bff54a1a1e61cb0e12
      2 33749cdacb1a90d18585eee9f41a3e8a
      2 3ce6c390c9b09b1a59283a41ce8a6849
      2 4d0f15f969c2a75014d3ea5aa566eda9
      2 4ebeb35932e1b9b07e2d36a5c82c078e
      2 4ed0c013bebc9e1f54eb026d94ef2fcd
      2 54695b59c6d3ff9c0f72376f952a978f
      2 54ce0406d1836b3fb6ad899870a27955
      2 58e819f5ef2bfc218e4e908d16058f5b
      2 593730c6a75517afd06e22b47fedf1f8
      2 63e0b96f9f9fff5f8d3821414ff1e6ef
      2 7c414f97eec049c0a2d1eb74c6a1f5ce
      2 7e5c0b919f8085141662ee559a21589d
      2 843792d56be0817bdccee0ff58e08702
      2 9b35fd2d92fe8e1c1db8e64aa2e29d71
      2 a071891bb1c81221da2e74927c657a3d
      2 a126a75faf0df8aca81bfeaca767d4e3
      2 a3843aa7108d75c87690749d6f05c320
      2 d1fa73b53d43cfff35ba9d08688f306a
      2 d88b043aeceb86b3c07e71eb87b3ce4c
      2 ecad7278c5b59084a873acbaf68921c1

I also tried to submit with -c and the following config but it got an error for unknown Apptainer option (version 1.2.2-1.el8)

singularity {
    engineOptions = "--disable-cache"
}

[tmoughamer]

It looks like singularity.ociAutoPull is recent addition to eliminate the duplication.