Fatal error when downloading sarek pipeline v2.7.1

[solcos]

Description of the bug

Singularity container retrieval failed when trying to download the nf-core/sarek pipeline. While making image from oci registry I got an error fetching image to cache and failed to get checksum for docker image.

Command used and terminal output

Input:
$ export NXF_SINGULARITY_CACHEDIR="/tmp/singularity_tmp/" && nf-core download sarek -r 2.7.1 --container singularity --compress none --force

Output:

INFO     Saving 'nf-core/sarek'                                                                                                                                                                                    
          Pipeline revision: '2.7.1'                                                                                                                                                                               
          Pull containers: 'singularity'                                                                                                                                                                           
          Using $NXF_SINGULARITY_CACHEDIR': /tmp/singularity_tmp/                                                                                                                                                  
          Output directory: 'nf-core-sarek-2.7.1'                                                                                                                                                                  
INFO     Downloading workflow files from GitHub                                                                                                                                                                    
INFO     Downloading centralised configs from GitHub                                                                                                                                                               
INFO     Found 4 containers                                                                                                                                                                                        
Pulling singularity images ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━  50% • 2/4 completed
{(params.annotation_cache && params.snpeff_cache) ? 'nfcore/sarek:2.7.1' : "nfcore/sareksnpeff:2.7.1.${params.genome}"}  ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━INFO     Singularity container retrieval fialed with the following error:                                                                                                                                          
INFO     FATAL:   While making image from oci registry: error fetching image to cache: failed to get checksum for docker://{(params.annotation_cache && params.snpeff_cache) ? 'nfcore/sarek:2.7.1' :              
         "nfcore/sareksnpeff:2.7.1.${params.genome}"}: unable to parse image name docker://{(params.annotation_cache && params.snpeff_cache) ? 'nfcore/sarek:2.7.1' : "nfcore/sareksnpeff:2.7.1.${params.genome}"}:
         invalid reference format                                                                                                                                                                                  
Pulling singularity images ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━  50% • 2/4 completed
{(params.annotation_cache && params.snpeff_cache) ? 'nfcor… FATAL:   While making image from oci registry: error fetching image to cache: failed to get checksum for docker://{(params.annotation_cache && params… 
CRITICAL The container "{(params.annotation_cache && params.snpeff_cache) ? 'nfcore/sarek:2.7.1' : "nfcore/sareksnpeff:2.7.1.${params.genome}"}" is unavailable.                                                   
         FATAL:   While making image from oci registry: error fetching image to cache: failed to get checksum for docker://{(params.annotation_cache && params.snpeff_cache) ? 'nfcore/sarek:2.7.1' :              
         "nfcore/sareksnpeff:2.7.1.${params.genome}"}: unable to parse image name docker://{(params.annotation_cache && params.snpeff_cache) ? 'nfcore/sarek:2.7.1' : "nfcore/sareksnpeff:2.7.1.${params.genome}"}:
         invalid reference format

Relevant files

System information

Nextflow version: 23.04.1.5866 Hardware: Desktop Executor: Local Container engine: Singularity OS: Linux Version of nf-core/sarek: 2.8

[FriederikeHanssen]

@maxulysse any idea here?

[maxulysse]

Oh yeah, snpeff and VEP containers are a mess. Sorry about that. Which genome are you interested in?

[solcos]

I am not interested in a specific reference genome, I will probably need to use different ones, but meanwhile it would be good to have the GRCh37 or 38 for testing. Thanks!

[maxulysse]

OK, so two solutions, either you download manually the containers for GRCh37/GRCh38 or you use some annotation cache

[maxulysse]

• docker.io/nfcore/sareksnpeff:2.7.1.GRCh37
• docker.io/nfcore/sareksnpeff:2.7.1.GRCh38
• docker.io/nfcore/sarekvep:2.7.1.GRCh37
• docker.io/nfcore/sarekvep:2.7.1.GRCh38

[solcos]

I'll try that and see if it works, thanks!