Centralize and synchronize GHAs

[maxulysse]

Description of feature

Both the modules repo and TEMPLATE use slightly different actions/workflows for common things, and they are slightly diverging more and more.

https://github.com/nf-core/modules/tree/master/.github/actions https://github.com/nf-core/tools/tree/dev/nf_core/pipeline-template/.github/actions

We have 2 get-shards, but 1 nf-test-action and 1 nf-test .

Similarly we have a update-gpu-snapshot.yml workflow and a update-sentieon-snapshot.yml workflow.

@edmundmiller, @mirpedrol and others raised the question about having a single update actions, which I think would be great to have in pipeline, and cover more than just updating snapshots for gpus and/or sentieon. I would just be wary about allowing to update everything as one can update unstable snapshots.

Also I noticed a bit of leftover java setup:

    - uses: actions/setup-java@c5195efecf7bdfc987ee8bae7a71cb8b11521c00 # v4
      with:
        distribution: "temurin"
        java-version: "17"

Similarly we have diverging actions from the template in some pipelines:

• https://github.com/nf-core/rnaseq/blob/dev/.github/workflows/cloud_tests_full.yml
• https://github.com/nf-core/rnaseq/blob/dev/.github/workflows/cloud_tests_small.yml
• https://github.com/nf-core/sarek/blob/dev/.github/workflows/cloudtest.yml
• https://github.com/nf-core/tools/blob/dev/nf_core/pipeline-template/.github/workflows/awstest.yml
• https://github.com/nf-core/tools/blob/dev/nf_core/pipeline-template/.github/workflows/awstestfull.yml