Workflow outputs only

[MattWellie]

This PR has been open a while, and has various stacked branches. Trying to tidy this up now.

The line count is kinda hideous, but much of that is adding a new nextflow schema file, or indenting blocks of script inside a script: parameter.

This doesn't change any app functionality, it's more like a massive linting for the pre-existing NF workflow. This might be the last commit to main before switching to a dev-branch centred development workflow.

Fixes

• Workflows were using a mix of WorkflowOutputs and PublishDir - this harmonises exclusively on Workflow outputs
• some workflow modules lacked an explicit script: declaration
• some workflow scripts lacked a pipefail instruction
• Dockerfile improvements (removing second htslib download, removing some layers, bumping to bcftools 1.23.1)
• Correction to the bcftools compression used when writing the merged VCF file
• Adds 3x retries to the ClinVar downloader process (fragile)
• Added nextflow_schema.json for Seqera/other platforms

Linting

• Channel. changed to channel. ("Channel" is deprecated in NextFlow according to nextflow lint)
• Unused elements in channel joins are prefixed with _
• Resource settings corrected in Groovy (e.g. '1 GB' -> 1.GB)

[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]

Pull request overview

Copilot reviewed 32 out of 32 changed files in this pull request and generated 5 comments.

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