docs(healthomics): Add Nextflow profile support and v26.04 guidance#146
Merged
nadetastic merged 1 commit intoJun 18, 2026
Merged
Conversation
HealthOmics supports Nextflow profiles across all engine versions and adds Nextflow v26.04 (strict v2 syntax, new plugins, agent mode, output summaries). Update steering files accordingly: - migration-guide-for-nextflow.md: Remove the contradictory "no profiles support" line in Phase 2. Rework Phase 5 to present top-level config, profile-based, and hybrid configurations as equally valid. Add Phase 6 covering the per-version plugin pre-install matrix, v26 strict-syntax migration options, deprecations, and unsupported v26 features. - running-a-workflow.md: Add an "Engine Settings" section documenting the Nextflow engineSettings keys (profile, syntaxVersion, outputFormat, agentMode) and profile application behavior. - workflow-development.md: Add short Engine Version and Profiles subsections linking to the matrix and Engine Settings reference.
markjschreiber
approved these changes
Jun 18, 2026
nadetastic
approved these changes
Jun 18, 2026
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Updates the aws-healthomics steering docs for Nextflow profile
support across all engine versions and Nextflow v26.04 (strict v2 syntax, new
pre-installed plugins, agent mode, output summaries).
support" line in Phase 2; reworks Phase 5 to present top-level,
profile-based, and hybrid configs as equally valid; adds Phase 6 (version
compatibility) with the per-version plugin pre-install matrix, v26
strict-syntax migration options, deprecations, and unsupported v26 features.
Nextflow
engineSettingskeys (profile,syntaxVersion,outputFormat,agentMode) and profile application behavior.subsections linking to the matrix and Engine Settings reference.