Update all deeptools conda environment YAML files to version 3.5.6

[bentyeh]

Updating to version 3.5.6 bypasses a previous bug where deeptools version 3.5.5 is not compatible with NumPy version 2, but the bioconda recipe (meta.yaml; https://github.com/bioconda/bioconda-recipes/blob/591f3c411db2cb334511f0f13e60b4d4d9cadb2f/recipes/deeptools/meta.yaml) for deeptools version 3.5.5 only specifies a lower limit on NumPy versions (numpy >=1.9.0), which inadvertently allows conda to install NumPy version 2 and deeptools version 3.5.5 in the same environment, leading to incompatibilities and pipeline errors.

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.
• Broadcast software version numbers to topic: versions - See version_topics
• Follow the naming conventions.
• Follow the parameters requirements.
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• 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

[SPPearce]

You'll need to also update the containers specified in the main.nf files, and rerun the tests to update the snapshots.
If you are able to, it'd be helpful to also swap to using topic channels: https://nf-co.re/docs/tutorials/migrate_to_topics/update_modules

[bentyeh]

@SPPearce Thank you for the comment. I'm new to nextflow and also not familiar with maintaining/updating containers. Would you mind pointing me to resources/tutorials about how to update the containers?

[SPPearce]

In the main.nf for each module, the containers for docker and singularity are defined:
https://github.com/nf-core/modules/blob/master/modules/nf-core/deeptools/plotpca/main.nf#L6-L8

    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        'https://depot.galaxyproject.org/singularity/deeptools:3.5.5--pyhdfd78af_0':
        'biocontainers/deeptools:3.5.5--pyhdfd78af_0' }"

These will need to be updated to the 3.5.6 version.
The command nf-core modules bump-versions deeptools/plotpca may do that for you (I haven't used it recently). Going to the depot.galaxyproject.org/singularity it suggests that deeptools:3.5.6--pyhdfd78af_0 is the correct build number/string for the new version.
Then you need to update the snapshots by running nf-core modules test deeptools/plotpca, as the version string will have changed.

[SPPearce]

Closing in favour of #10037 10037