Collection of small changes

[MattWellie]

Purpose

• Latest changes to CPG-Flow mean we need to provide a workflow name
• AnnotateCohort MT should be kept in long-term storage (still subject to auditing)
• Combiner stage can accidentally re-run if the VDS exists but the temp directory has lapsed
• Replaces Combiner TmpDir as a String, not Path #13

Proposed Changes

• move output path of annotate cohort out of tmp
• add workflow name to both invocation scripts (plus set cpg-flow dependency version as >=1)
• include changes on Combiner TmpDir as a String, not Path #13 (set combiner temp directory as a String, so CPG-Flow won't test for its existence)
• bump version

Checklist

• Related GitHub Issue created
• Tests covering new change
• Linting checks pass

[Copilot]

Pull Request Overview

This PR contains multiple maintenance updates to ensure compatibility with the latest CPG-Flow version and improve file organization. The changes address workflow naming requirements, move outputs from temporary to permanent storage, and fix parameter handling issues.

Key changes:

• Add required workflow names to CPG-Flow invocations
• Move AnnotateCohort output from temporary to permanent storage
• Fix combiner stage parameter handling to prevent accidental re-runs

Reviewed Changes

Copilot reviewed 7 out of 7 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
src/cpg_seqr_loader/stages.py	Updated combiner temp directory handling and moved AnnotateCohort output location
src/cpg_seqr_loader/jobs/CombineGvcfsIntoVds.py	Added import and converted string parameter back to Path object
src/cpg_seqr_loader/full_workflow.py	Added required workflow name parameter to run_workflow call
src/cpg_seqr_loader/first_workflow.py	Added required workflow name parameter to run_workflow call
pyproject.toml	Updated version and CPG-Flow dependency requirements
README.md	Updated version references in documentation
.github/workflows/docker.yaml	Updated version for Docker builds

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