Update CELLRANGER_MKGTF

[lucacozzuto]

Wrong container

PR checklist

Closes #XXX

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the module conventions in the contribution docs
• If necessary, include test data in your PR.
• Remove all TODO statements.
• Emit the versions.yml file.
• Follow the naming conventions.
• Follow the parameters requirements.
• Follow the input/output options guidelines.
• Add a resource label
• Use BioConda and BioContainers if possible to fulfil software requirements.
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  • For modules:
    • nf-core modules test <MODULE> --profile docker
    • nf-core modules test <MODULE> --profile singularity
    • nf-core modules test <MODULE> --profile conda
  • For subworkflows:
    • nf-core subworkflows test <SUBWORKFLOW> --profile docker
    • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
    • nf-core subworkflows test <SUBWORKFLOW> --profile conda

[maxulysse]

no need to specify quay.io as it's the default registry for all nf-core

[lucacozzuto]

But is it the same also when using it outside a nf-core pipeline? I did because it was going to dockerhub...

[maxulysse]

all nf-core modules have this.

which is why we have this in the template:
https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/nextflow.config#L226-L233

[maxulysse]

outside of nf-core I would recommend either using this default registry as well, or patching the module in the pipeline

[maxulysse]

or overriding the container declaration in the config file

[lucacozzuto]

Ok, thank you!

[lucacozzuto]

Just a last comment: should this declaration be placed inside the modules.config that is produced by the nf-core tools?

[maxulysse]

For me this would fit more in the conf/base.config.
conf/modules.config is more for args and publishdir
But really any place should work.

[lucacozzuto]

Yes, how can I / we suggest this?