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Allocate more memory to PIXELATOR_DENOSIE for 8k_cell runs#225

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fix/increase-denoise-memory-allocation
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Allocate more memory to PIXELATOR_DENOSIE for 8k_cell runs#225
ptajvar wants to merge 3 commits into
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fix/increase-denoise-memory-allocation

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@ptajvar

@ptajvar ptajvar commented Jun 9, 2026

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Denoise currently requires more memory to run for the 8K-cell samples. This PR increases the first iteration memory allocation from 64GB (process_high value) to 256GB.

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/pixelator branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
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  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
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@ptajvar ptajvar requested a review from a team as a code owner June 9, 2026 08:34
@ptajvar ptajvar requested a review from Copilot June 9, 2026 08:34
@ptajvar ptajvar requested a review from johandahlberg June 9, 2026 08:35
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github-actions Bot commented Jun 9, 2026 •
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nf-core pipelines lint overall result: Passed ✅

Posted for pipeline commit 6e527f1

+| ✅ 231 tests passed       |+
#| ❔   9 tests were ignored |#
Details

❔ Tests ignored:

  • files_exist - File is ignored: assets/multiqc_config.yml
  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: conf/igenomes_ignored.config
  • files_exist - File is ignored: tests/default.nf.test
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-pixelator_logo_light.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • multiqc_config - multiqc_config

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.2
  • Run at 2026-06-09 08:39:52

Copilot AI reviewed Jun 9, 2026
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Pull request overview

This PR aims to increase resource allocation for the denoise step when running the 8k-cell configuration, addressing out-of-memory failures by raising the memory request for the first attempt.

Changes:

  • Add a per-process resource override in cells_8k for the Pixelator denoise step.
  • Increase denoise memory allocation to 256 GB (scaled by task.attempt).

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Comment thread conf/cells_8k.config Outdated
Comment thread conf/cells_8k.config Outdated
ptajvar and others added 2 commits June 9, 2026 10:37
@ptajvar
Potential fix for pull request finding
8eeea1a 
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
@ptajvar
back to process_high 16h default time allocation
6e527f1 
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
@ptajvar ptajvar requested a review from Aratz June 9, 2026 08:42
@ptajvar ptajvar marked this pull request as draft June 15, 2026 09:53
@ptajvar ptajvar closed this Jun 15, 2026
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@johandahlberg johandahlberg Awaiting requested review from johandahlberg

@Aratz Aratz Awaiting requested review from Aratz

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@ptajvar