Workflow outputs only

[MattWellie]

Fixes

• Workflows were using a mix of WorkflowOutputs and PublishDir

Proposed Changes

• Migrates entirely to WorkflowOutputs

[Copilot]

Pull request overview

This PR completes the migration of the Talos Nextflow pipeline to use Nextflow's WorkflowOutputs mechanism (publish: blocks and output {} directives) exclusively for all output file handling, removing publishDir directives from every process module. It also adds a nextflow_schema.json parameter schema and a ResummariseRawSubmissions resource configuration block.

Changes:

• Removes all publishDir (and commented-out // publishDir) directives from every annotation, talos, and prep process module, delegating output publishing to the workflow-level output {} blocks.
• Removes params.outdir from nextflow.config and adds a ResummariseRawSubmissions resource requirements block.
• Adds nextflow_schema.json documenting all pipeline parameters.

Reviewed changes

Copilot reviewed 15 out of 15 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
nextflow.config	Removes the outdir parameter; adds ResummariseRawSubmissions resource block
nextflow_schema.json	New file: JSON Schema describing all pipeline parameters
nextflow/modules/talos/ValidateMOI/main.nf	Removes publishDir directive
nextflow/modules/talos/UnifiedPanelAppParser/main.nf	Removes publishDir directive
nextflow/modules/talos/StartupChecks/main.nf	Removes commented-out publishDir directive
nextflow/modules/talos/RunHailFiltering/main.nf	Removes publishDir directive
nextflow/modules/talos/HPOFlagging/main.nf	Removes publishDir directive and associated comment
nextflow/modules/talos/CreateTalosHTML/main.nf	Removes publishDir directive
nextflow/modules/prep/CreateRoiFromGff3/main.nf	Condenses two-line comment to one line
nextflow/modules/annotation/SplitVcf/main.nf	Removes commented-out publishDir directive
nextflow/modules/annotation/NormaliseAndRegionFilterVcf/main.nf	Removes commented-out publishDir directive
nextflow/modules/annotation/MergeVcfsWithBcftools/main.nf	Removes commented-out publishDir directive
nextflow/modules/annotation/AnnotatedVcfIntoMatrixTable/main.nf	Removes publishDir directive
nextflow/modules/annotation/AnnotateWithEchtvar/main.nf	Removes commented-out publishDir directive
nextflow/modules/annotation/AnnotateCsqWithBcftools/main.nf	Removes commented-out publishDir directive

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[Copilot]

The default value for gnomad_zip on line 106 contains a Nextflow parameter interpolation expression: "${params.large_files}/gnomad_4.1_region_merged_GRCh38_whole_genome". This is not a valid JSON Schema default value — JSON Schema default must be a literal value, not a template string. The ${params.large_files} expression will be stored and interpreted as a literal string by any JSON Schema validator or nf-core schema tooling, rather than being interpolated at runtime. The actual default is set in nextflow.config (line 56: gnomad_zip = "${params.large_files}/gnomad_4.1_region_merged_GRCh38_whole_genome"). The default in the schema should either be omitted (leaving the actual default to nextflow.config) or replaced with a descriptive placeholder string like "<large_files>/gnomad_4.1_region_merged_GRCh38_whole_genome" to indicate the path pattern without implying runtime interpolation.

Suggested change

	"default": "${params.large_files}/gnomad_4.1_region_merged_GRCh38_whole_genome",
	"default": "<large_files>/gnomad_4.1_region_merged_GRCh38_whole_genome",