[FEATURE] Update modules to remove undocumented task.ext fields

Is your feature request related to a problem? Please describe

task.ext fields were introduced allow users to override developer settings in pipelines. However some modules are simply using them as an alternative input: method for parameters that don't always need to be supplied.

% find modules -name "*.nf" -exec grep -H "task.ext." {} \; | grep -vE "task\.ext\.(singularity|args|prefix|when|suffix)"
modules/nf-core/picard/fixmateinformation/main.nf:    def STRINGENCY = task.ext.stringency ?: "STRICT"
modules/nf-core/artic/minion/main.nf:    def hd5_plugin_path = task.ext.hd5_plugin_path ? "export HDF5_PLUGIN_PATH=${task.ext.hd5_plugin_path}" : "export HDF5_PLUGIN_PATH=/usr/local/lib/python3.6/site-packages/ont_fast5_api/vbz_plugin"
modules/nf-core/fgbio/zipperbams/main.nf:    def compression = task.ext.compression ?: '0'
modules/nf-core/jupyternotebook/main.nf:    def parametrize = (task.ext.parametrize == null) ?  true : task.ext.parametrize
modules/nf-core/jupyternotebook/main.nf:    def implicit_params = (task.ext.implicit_params == null) ? true : task.ext.implicit_params
modules/nf-core/jupyternotebook/main.nf:    def meta_params = (task.ext.meta_params == null) ? true : task.ext.meta_params
modules/nf-core/jupyternotebook/main.nf:    def kernel   = task.ext.kernel ?: '-'
modules/nf-core/rmarkdownnotebook/main.nf:    def parametrize = (task.ext.parametrize == null) ?  true : task.ext.parametrize
modules/nf-core/rmarkdownnotebook/main.nf:    def implicit_params = (task.ext.implicit_params == null) ? true : task.ext.implicit_params
modules/nf-core/rmarkdownnotebook/main.nf:    def meta_params = (task.ext.meta_params == null) ? true : task.ext.meta_params
modules/nf-core/plink2/vcf2bgen/main.nf:    def reffirst = bgen_reffirst || task.ext.reffirst ? "ref-first" : ""
modules/nf-core/plink2/vcf2bgen/main.nf:    def dosage = task.ext.dosage_field ? task.ext.dosage_field : dosage_field
modules/nf-core/plink2/vcf2bgen/main.nf:    def sample_name_opt = task.ext.sample_name_mode ? task.ext.sample_name_mode : sample_name_mode
modules/nf-core/hmmer/eslreformat/main.nf:    def postproc = task.ext.postprocessing ?: ""
modules/nf-core/cellbender/merge/main.nf:    output_layer = task.ext.output_layer ?: "cellbender"
modules/nf-core/cellbender/removebackground/main.nf:    container "${ task.ext.use_gpu ? 'us.gcr.io/broad-dsde-methods/cellbender:0.3.2' :
modules/nf-core/cellbender/removebackground/main.nf:    use_gpu = task.ext.use_gpu ? "--cuda" : ""
modules/nf-core/bedtools/groupby/main.nf:    def summary_col = task.ext.summary_col ? "-c ${task.ext.summary_col}" : "-c 5"
modules/nf-core/scvitools/scar/main.nf:    input_layer = task.ext.input_layer ?: "X"
modules/nf-core/scvitools/scar/main.nf:    output_layer = task.ext.output_layer ?: "scar"
modules/nf-core/scvitools/scar/main.nf:    max_epochs = task.ext.max_epochs ?: ""
modules/nf-core/scvitools/solo/main.nf:    container "${ task.ext.use_gpu ? 'docker.io/nicotru/scvitools-gpu:cuda-12' :
modules/nf-core/scvitools/solo/main.nf:    batch_key = task.ext.batch_key ?: ""
modules/nf-core/scvitools/solo/main.nf:    max_epochs = task.ext.max_epochs ?: ""
modules/nf-core/metaspace/converter/main.nf:    database_name    = task.ext.database_name ?: "HMDB"
modules/nf-core/metaspace/converter/main.nf:    database_version = task.ext.database_version ?: "v4"
modules/nf-core/metaspace/converter/main.nf:    fdr              = task.ext.fdr ?: "0.1"
modules/nf-core/metaspace/converter/main.nf:    use_tic          = task.ext.use_tic ?: "true"
modules/nf-core/metaspace/converter/main.nf:    metadata_as_obs  = task.ext.metadata_as_obs ?: "false"
modules/nf-core/sentieon/dedup/main.nf:    def metrics = task.ext.metrics ?: "${prefix}.metrics"
modules/nf-core/sentieon/dedup/main.nf:    def metrics = task.ext.metrics ?: "${prefix}.metrics"
modules/nf-core/icountmini/segment/main.nf:    def regions_prefix = task.ext.regions_prefix ?: "${gtf.simpleName}"
modules/nf-core/icountmini/segment/main.nf:    def regions_prefix = task.ext.regions_prefix ?: "${gtf.simpleName}"

Describe the solution you'd like

The modules should be refactored so the "non-standard" task.ext fields are moved to input: and documented in the meta.yml so pipeline developers know what to set.

Describe alternatives you've considered

No response

Additional context

No response

Start with the listed modules/*/main.nf files and their corresponding meta.yml files, using the grep command in the issue to inventory non-standard task.ext fields. Check how each field is currently consumed and how module inputs are documented. Done means the listed fields are exposed through input: and documented in meta.yml, with no undocumented non-standard task.ext usage remaining.