Installation issues - airrflow pipeline

[pnatarajan9]

Description of the bug

Airrflow - https://github.com/nf-core/airrflow

CRITICAL The container "nf-core/cellranger:7.1.0" is unavailable.
WARNING: Couldn't use cached digest for registry: HEAD https://index.docker.io/v2/nf-core/cellranger/manifests/7.1.0:
unexpected status code 401 Unauthorized (HEAD responses have no body, use GET for details)
WARNING: Falling back to direct digest.
FATAL: While making image from oci registry: error fetching image to cache: failed to get checksum for
docker://nf-core/cellranger:7.1.0: GET https://index.docker.io/v2/nf-core/cellranger/manifests/7.1.0: UNAUTHORIZED:
authentication required; [map[Action:pull Class: Name:nf-core/cellranger Type:repository]]

Command used and terminal output

No response

Relevant files

No response

System information

Nextflow version - 23.04.1 nf-core version: 2.7.2 Ubuntu 22.04.4 LTS (GNU/Linux 6.5.0-28-generic x86_64) nf-core airrflow version 4.1.0

[ggabernet]

Hi @pnatarajan9 ,

I could not reproduce this error, I just tried pulling this container and it is available for me. Could you try if this works for you:

docker pull nfcore/cellranger:7.1.0

If this doesn't work, it could be that docker is not properly installed or that your system has no internet connection, which is needed to pull the containers.

If this works, but airrflow continues to fail, could you share the full command you used to run it?

[pnatarajan9]

Full command used and the errors:

$ nf-core download airrflow --outdir dev --singularity-cache-only --container singularity

? Select release / branch: 4.1.0 [release]

If transferring the downloaded files to another system, it can be convenient to have everything compressed in a single file. This is not recommended when downloading Singularity images, as it can take a long time and saves very little space. ? Choose compression type: none INFO Saving 'nf-core/airrflow'
Pipeline revision: '4.1.0'
Pull containers: 'singularity'
Using $NXF_SINGULARITY_CACHEDIR': /ccbbcoded/ccbb_software/software/nfcore/singularity
Output directory: 'dev'
INFO Downloading workflow files from GitHub
INFO Downloading centralised configs from GitHub
INFO Found 12 containers
Pulling singularity images ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━ 92% • 11/12 completed nf-core/cellranger:7.1.0 WARNING: Falling back to direct digest. ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━Pulling singularity images ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━ 92% • 11/12 completed nf-core/cel… FATAL: While making image from oci registry: error fetching image to cache: failed to get checksum for docker://nf-cor… INFO WARNING: Couldn't use cached digest for registry: HEAD https://index.docker.io/v2/nf-core/cellranger/manifests/7.1.0:
unexpected status code 401 Unauthorized (HEAD responses have no body, use GET for details)
WARNING: Falling back to direct digest.
FATAL: While making image from oci registry: error fetching image to cache: failed to get checksum for
docker://nf-core/cellranger:7.1.0: GET https://index.docker.io/v2/nf-core/cellranger/manifests/7.1.0: UNAUTHORIZED:
authentication required; [map[Action:pull Class: Name:nf-core/cellranger Type:repository]]
Pulling singularity images ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━ 92% • 11/12 completed nf-core/cel… FATAL: While making image from oci registry: error fetching image to cache: failed to get checksum for docker://nf-cor… CRITICAL The container "nf-core/cellranger:7.1.0" is unavailable.
WARNING: Couldn't use cached digest for registry: HEAD https://index.docker.io/v2/nf-core/cellranger/manifests/7.1.0:
unexpected status code 401 Unauthorized (HEAD responses have no body, use GET for details)
WARNING: Falling back to direct digest.
FATAL: While making image from oci registry: error fetching image to cache: failed to get checksum for
docker://nf-core/cellranger:7.1.0: GET https://index.docker.io/v2/nf-core/cellranger/manifests/7.1.0: UNAUTHORIZED:
authentication required; [map[Action:pull Class: Name:nf-core/cellranger Type:repository]]

[ggabernet]

Hi @pnatarajan9,

I tested this command with the latest version of the nf-core tools (2.14.1) and it is working for me:

nf-core download airrflow --outdir dev --container-system singularity

                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 2.14.1 - https://nf-co.re

WARNING  Could not find GitHub authentication token. Some API requests may fail.                                                                   
? Select release / branch: 4.1.0  [release]
? Include the nf-core's default institutional configuration files into the download? No

Nextflow and nf-core can use an environment variable called $NXF_SINGULARITY_CACHEDIR that is a path to a directory where remote Singularity images
are stored. This allows downloaded images to be cached in a central location.
? Define $NXF_SINGULARITY_CACHEDIR for a shared Singularity image download folder? [y/n]: 
Please enter Y or N
? Define $NXF_SINGULARITY_CACHEDIR for a shared Singularity image download folder? [y/n]: n

If transferring the downloaded files to another system, it can be convenient to have everything compressed in a single file.
This is not recommended when downloading Singularity images, as it can take a long time and saves very little space.
? Choose compression type: tar.gz
INFO     Saving 'nf-core/airrflow'                                                                                                                 
          Pipeline revision: '4.1.0'                                                                                                               
          Use containers: 'singularity'                                                                                                            
          Container library: 'quay.io'                                                                                                             
          Output file: 'dev.tar.gz'                                                                                                                
          Include default institutional configuration: 'False'                                                                                     
INFO     Downloading workflow files from GitHub                                                                                                    
INFO     Processing workflow revision 4.1.0, found 13 container images in total.                                                                   
Pulling singularity images ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% • 13/13 completed
INFO     Compressing output into archive                                                                                                           
INFO     Command to extract files: tar -xzf dev.tar.gz                                                                                             
INFO     MD5 checksum for 'dev.tar.gz': 2d325c504ef1632a7627b0ea6048abf9 

Inside the tar archive the cellranger container was also downloaded properly. Did you try updating the nf-core tools?

[pnatarajan9]

Yes, we tried the installation with the latest version of the nf-core tools (2.14.1) and are getting similar errors:

[pnatarajan9]

Update: We were able to install airrflow with the nf-core version 2.14.1 in different compute environment. Thank you for your help!

[ggabernet]

Great to hear that your issue has been solved!