Fix config

[muffato]

In this pull-request:

• I added the GitHub Actions files to test the pipelines on the Sanger farm, as @gq1 did on https://github.com/sanger-tol/insdcdownload/pull/4
• I pinned the version of nf-core used in the tests to 2.6
• I updated the nf-core config file to ignore template files that are modified on purpose (typically because they're branded sanger-tol rather than nf-core)
• I added the when section to various modules. That was just a warning, not an error, but an easy one to address
• I recorded two parameters in nextflow_schema.json

PR checklist

• [ ] 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 pipeline conventions in the contribution docs- [ ] If necessary, also make a PR on the nf-core/blobtoolkit branch on the nf-core/test-datasets repository.
• [ ] Make sure your code lints (nf-core lint).
• [ ] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• [ ] Usage Documentation in docs/usage.md is updated.
• [ ] Output Documentation in docs/output.md is updated.
• [ ] CHANGELOG.md is updated.
• [ ] README.md is updated (including new tool citations and authors/contributors).

[muffato]

@zb32 : can we look at docs/parameters.md together tomorrow ? When I run prettier on it, it doesn't look broken. I just want to check what the problem is. If needed we can add docs/parameters.md to .prettierignore to skip that error.

[gq1]

The full test failed on the Tower: https://tower.nf/orgs/sanger-tol/workspaces/github-ci/watch/3Kk1DcZ0AzF9ZC

Error executing process > 'NFCORE_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:BUSCO (GCA_927399515.1)'

Caused by:
  Failed to pull singularity image
  command: singularity pull  --name depot.galaxyproject.org-singularity-busco-5.4.3--pyhdfd78af_0.img.pulling.1675942416800 https://depot.galaxyproject.org/singularity/busco:5.4.3--pyhdfd78af_0 > /dev/null
  status : 143
  message:
    INFO:    Downloading network image

Manually copy the image from mm49's cache directory and re-run the action from Github:

https://tower.nf/orgs/sanger-tol/workspaces/github-ci/watch/4A9fcaFqLGAzFb