Singularity container symlinks not consistently created

[muffato]

Description of the bug

(discussed on Slack)

Example with

nf-core pipelines download nf-core/fetchngs --revision 1.11.0 --download-configuration --compress none --container-system singularity --container-cache-utilisation copy

1. If NXF_SINGULARITY_CACHEDIR is not set, symlinks are always created in the download directory after download (L1352 and L1463: in both cases, output_path is set to out_path because cache_path is not set)
2. If NXF_SINGULARITY_CACHEDIR is set, symlinks are created in the download directory only if the container is copied from the cache. Otherwise, symlinks are only created in the cache directory (still L1352 and L1463 but this time, output_path is set to cache_path).

For instance, if NXF_SINGULARITY_CACHEDIR is set and complete, I get files + symlinks under nf-core-fetchngs_1.11.0/singularity-images/

depot.galaxyproject.org-singularity-mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a-2f4a4c900edd6801ff0068c2b3048b4459d119eb-0.img -> ./singularity-mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a-2f4a4c900edd6801ff0068c2b3048b4459d119eb-0.img
depot.galaxyproject.org-singularity-python-3.9--1.img -> ./singularity-python-3.9--1.img
depot.galaxyproject.org-singularity-sra-tools-2.11.0--pl5321ha49a11a_3.img -> ./singularity-sra-tools-2.11.0--pl5321ha49a11a_3.img
depot.galaxyproject.org-singularity-sra-tools-3.0.8--h9f5acd7_0.img -> ./singularity-sra-tools-3.0.8--h9f5acd7_0.img
depot.galaxyproject.org-singularity-synapseclient-2.7.1--pyh7cba7a3_0.img -> ./singularity-synapseclient-2.7.1--pyh7cba7a3_0.img
depot.galaxyproject.org-singularity-ubuntu-20.04.img -> ./singularity-ubuntu-20.04.img
quay.io-singularity-mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a-2f4a4c900edd6801ff0068c2b3048b4459d119eb-0.img -> ./singularity-mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a-2f4a4c900edd6801ff0068c2b3048b4459d119eb-0.img
quay.io-singularity-python-3.9--1.img -> ./singularity-python-3.9--1.img
quay.io-singularity-sra-tools-2.11.0--pl5321ha49a11a_3.img -> ./singularity-sra-tools-2.11.0--pl5321ha49a11a_3.img
quay.io-singularity-sra-tools-3.0.8--h9f5acd7_0.img -> ./singularity-sra-tools-3.0.8--h9f5acd7_0.img
quay.io-singularity-synapseclient-2.7.1--pyh7cba7a3_0.img -> ./singularity-synapseclient-2.7.1--pyh7cba7a3_0.img
quay.io-singularity-ubuntu-20.04.img -> ./singularity-ubuntu-20.04.img

singularity-mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a-2f4a4c900edd6801ff0068c2b3048b4459d119eb-0.img
singularity-python-3.9--1.img
singularity-sra-tools-2.11.0--pl5321ha49a11a_3.img
singularity-sra-tools-3.0.8--h9f5acd7_0.img
singularity-synapseclient-2.7.1--pyh7cba7a3_0.img
singularity-ubuntu-20.04.img

On the other hand, If NXF_SINGULARITY_CACHEDIR is set but empty, the cache has the files and the symlinks as above, but I get only files under nf-core-fetchngs_1.11.0/singularity-images/

$ ls nf-core-fetchngs_1.11.0/singularity-images/ 
singularity-mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a-2f4a4c900edd6801ff0068c2b3048b4459d119eb-0.img
singularity-python-3.9--1.img
singularity-sra-tools-2.11.0--pl5321ha49a11a_3.img
singularity-sra-tools-3.0.8--h9f5acd7_0.img
singularity-synapseclient-2.7.1--pyh7cba7a3_0.img
singularity-ubuntu-20.04.img

Command used and terminal output

nf-core pipelines download nf-core/fetchngs --revision 1.11.0 --download-configuration --compress none --container-system singularity --container-cache-utilisation copy

System information

Tested on tools v2.14.1 and dev