Template update to nf-core/tools 4.1.0 and re-linting #66

The pipeline is on template 4.0.2 and lints cleanly with nf-core/tools 4.0.2. With tools 4.1.0, nf-core pipelines lint --release reports 5 failures, all of which come from the template version:

• files_exist: .github/workflows/pr-comment.yml missing
• files_unchanged: .github/workflows/branch.yml and .github/workflows/linting.yml differ from the template
• container_configs: conf/containers_conda_lock_files_{amd64,arm64}.config out of date

To do

• Merge the automated template-sync branches nf-core-template-merge-4.0.3 and nf-core-template-merge-4.1.0 into dev (resolve conflicts in favour of our pipeline code); via Important! Template update for nf-core/tools v4.1.0 #65
• Set nf_core_version: 4.1.0 in .nf-core.yml
• Regenerate container configs: nf-core pipelines lint --fix container_configs
• nf-core modules update --all (samtools/sort, samtools/index) and nf-core subworkflows update --all (utils_nextflow_pipeline, utils_nfcore_pipeline, utils_nfschema_plugin); this also fixes the only nextflow lint error (groovy.json.JsonGenerator.Options undefined in utils_nextflow_pipeline/main.nf)
• Update the nf-test snapshot if module versions change
• Address the ~117 nextflow lint strict-syntax warnings, mostly in workflows/deepmutscan.nf
• Re-run nf-core pipelines lint --release: only the expected Zenodo badge warning should remain