Cc nf corrections

[MattWellie]

Fixes

• Various issues identified through analysis with claude.
• Some are soft inconsistencies (mixed use of case, missing shebangs, missing nextflow.enable.dsl=2 etc.)
• Some are hard bugs (bcftools output written using wrong flag)
• Some are incomplete changes (mix of workflow publishing and output directives, addressed by unmerged Workflow outputs only #645)
• Some are functional but incorrect (Memory setting of "1 GB" instead of 1.GB - same result, but though string parsing instead of plain Groovy
• Some are ideal but not essential (set -euo pipefail added to all script blocks), rm -f to prevent failure if files (which are definitely written) stop being written
• Some corrections (indexing files during correct stage and passing VCF with index, instead of indexing an input, so the index would be lost in the working directory)
• Adds missing script: directives to some files

Proposed Changes

• Solve all of the above. Test in progress

Checklist

• ChangeLog Updated
• Version Bumped
• Related Issue created
• Tests covering new change
• Linting checks pass

[Copilot]

Pull request overview

This PR cleans up and standardizes the Talos Nextflow pipelines by moving further toward DSL2 + workflow outputs, tightening bash execution behavior across modules, and correcting several workflow/module inconsistencies.

Changes:

• Standardize Nextflow DSL2 usage and workflow outputs (removing publishDir usage across many processes).
• Harden module script execution (set -euo pipefail), adjust indexing/IO wiring for some VCF flows, and fix a bcftools output mode bug.
• Add a nextflow_schema.json for parameter documentation/validation and update docs to reflect outputDir usage.

Reviewed changes

Copilot reviewed 30 out of 30 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
talos_only.nf	Adds DSL2/shebang and adjusts how cohort MT inputs are discovered for TALOS-only runs.
src/talos/cpg_internal_scripts/cpgflow_jobs/make_config.py	Comment wording/grammar tweak.
nextflow_schema.json	Introduces a Nextflow params JSON schema for the pipeline.
nextflow/modules/talos/ValidateMOI/main.nf	Removes publishDir; adds stricter bash options.
nextflow/modules/talos/UnifiedPanelAppParser/main.nf	Removes publishDir; adds missing script: + stricter bash options.
nextflow/modules/talos/StartupChecks/main.nf	Removes publishDir comment; strengthens bash error handling.
nextflow/modules/talos/RunHailFiltering/main.nf	Removes publishDir; adds stricter bash options.
nextflow/modules/talos/HPOFlagging/main.nf	Removes publishDir; adds missing script: + stricter bash options.
nextflow/modules/talos/CreateTalosHTML/main.nf	Removes publishDir; adds stricter bash options.
nextflow/modules/prep/ResummariseRawSubmissions/main.nf	Emits VCF+index as a tuple, adds tabix indexing, and hardens cleanup.
nextflow/modules/prep/ParseManeIntoJson/main.nf	Adds stricter bash options.
nextflow/modules/prep/ParseAlphaMissense/main.nf	Adds stricter bash options.
nextflow/modules/prep/MakeClinvarbitrationPm5/main.nf	Adds stricter bash options and makes cleanup tolerant.
nextflow/modules/prep/EncodeAlphaMissense/main.nf	Adds stricter bash options.
nextflow/modules/prep/DownloadPanelApp/main.nf	Adds stricter bash options.
nextflow/modules/prep/DownloadClinVarFiles/main.nf	Adds stricter bash options in shell: block.
nextflow/modules/prep/CreateRoiFromGff3/main.nf	Adds stricter bash options; minor comment adjustment.
nextflow/modules/prep/ConvertSpliceVarDb/main.nf	Adds stricter bash options.
nextflow/modules/prep/AnnotateClinvarWithBcftools/main.nf	Updates input signature to include VCF index; adds stricter bash options.
nextflow/modules/annotation/SplitVcf/main.nf	Adds stricter bash options.
nextflow/modules/annotation/NormaliseAndRegionFilterVcf/main.nf	Adds stricter bash options and indexes the input VCF.
nextflow/modules/annotation/MergeVcfsWithBcftools/main.nf	Adds stricter bash options and fixes bcftools output mode to match .vcf.bgz.
nextflow/modules/annotation/AnnotatedVcfIntoMatrixTable/main.nf	Adds stricter bash options; makes checkpoint cleanup tolerant.
nextflow/modules/annotation/AnnotateWithEchtvar/main.nf	Adds stricter bash options.
nextflow/modules/annotation/AnnotateCsqWithBcftools/main.nf	Adds stricter bash options and indexes before csq.
nextflow/annotation.nf	Fixes Channel.fromPath capitalization/usage consistency.
nextflow.config	Removes outdir, normalizes resource units to X.GB, and updates process resources.
main.nf	Explicitly enables DSL2.
docs/NextflowConfiguration.md	Removes outdir docs; documents outputDir instead.
README.md	Updates output path documentation to use {outputDir}.

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[Copilot]

Channel.fromPath(...) inside the .map { row -> tuple(...) } produces a nested channel, but downstream TALOS inputs expect a concrete path/collection (e.g., the list of *.mt directories), not a Channel. This will break channel typing/tuple structure at runtime. Build the mts value as a path collection (e.g., via files(...) with type:'dir') and avoid creating a new channel per row; also prefer workflow.outputDir here (the bare outputDir identifier is not consistently used elsewhere in this script).

Suggested change

	Channel.fromPath("${outputDir}/${row.cohort}_outputs/*.mt", checkIfExists: true),
	files("${workflow.outputDir}/${row.cohort}_outputs/*.mt", type: 'dir'),