feat(#11): consolidate UCR HPCC institutional profile - #22
Merged
Conversation
Move all UCR-specific settings out of the portable pipeline profile and
into conf/provision_ucr_hpcc.config:
profile_annotate.config — now contains only cpus/memory/time (site-agnostic).
queue = / clusterOptions = removed from all withName blocks.
Non-UCR SLURM users can run -profile annotate,slurm without overrides.
provision_ucr_hpcc.config — now owns two things:
1. Tool provisioning: withLabel beforeScript blocks (Lmod module loads).
Added earlgrey / repeatmask / select / deliver labels (previously missing).
2. SLURM partition routing: withName queue= / clusterOptions= for every
process, including EarlGrey path processes.
profile_earlgrey.config — beforeScript / queue / clusterOptions removed from
withLabel blocks; only cpus/memory/time remain (portable resource sizes).
modules/local/earlgrey_build_lib.nf, repeatmask_strain.nf — removed inline
`module load` from script bodies; environment comes from beforeScript per
the established pattern (scripts contain NO module load lines).
docs/adding_a_site.md — new: step-by-step guide for adapting the institutional
profile to a new HPC site (copy file, replace module names, replace queue
names, register profile).
Stub gates: tantan 15/0, EarlGrey 16/0.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01AbWwmm9v6dJn13sgAJn3Sa
NF 25.10.0 strict config validation rejects withName blocks that contain only comments and no directives. The block was a no-op placeholder. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01AbWwmm9v6dJn13sgAJn3Sa
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
1 participant
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.
Summary
conf/profile_annotate.confignow portable — allqueue =/clusterOptions =removed; contains only cpus/memory/time. Non-UCR SLURM users can run `-profile annotate,slurm` without overrides.conf/provision_ucr_hpcc.confignow owns both UCR concerns: Lmod `beforeScript` blocks (added missing `earlgrey`/`repeatmask`/`select`/`deliver` labels) + SLURM partition routing (`withName` section with every process queue assignment and clusterOptions).Test plan
🤖 Generated with Claude Code
https://claude.ai/code/session_01AbWwmm9v6dJn13sgAJn3Sa