Fix typo in openms_peak_picker processOption value by Copilot · Pull Request #689 · bigbio/quantms

Copilot · 2026-03-25T20:41:45Z

PeakPickerHiRes -processOption was passed inmermory instead of the valid value inmemory, causing the option to be silently ignored or rejected.

modules/local/openms/openms_peak_picker/main.nf: corrected "inmermory" → "inmemory"

# Before
in_mem = params.peakpicking_inmemory ? "inmermory" : "lowmemory"

# After
in_mem = params.peakpicking_inmemory ? "inmemory" : "lowmemory"

Original prompt

This section details on the original issue you should resolve

<issue_title>Typo in openms_peak_picker</issue_title>
<issue_description>### Description of the bug

inmermory -> inmemory

reference

quantms/modules/local/openms/openms_peak_picker/main.nf

Line 22 in e719f43

in_mem = params.peakpicking_inmemory ? "inmermory" : "lowmemory"

Command used and terminal output
Relevant files

No response

System information

No response</issue_description>

<agent_instructions>make the one-line change.</agent_instructions>

Comments on the Issue (you are @copilot in this section)

Fixes Typo in openms_peak_picker #688

📱 Kick off Copilot coding agent tasks wherever you are with GitHub Mobile, available on iOS and Android.

Co-authored-by: enryH <2833836+enryH@users.noreply.github.com> Agent-Logs-Url: https://github.com/bigbio/quantms/sessions/ef73a74e-d614-4f35-b4af-4c6994dd711d

github-actions · 2026-03-26T07:46:05Z

`nf-core pipelines lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit aaa0b91

+| ✅ 110 tests passed       |+
#| ❔  19 tests were ignored |#
!| ❗   3 tests had warnings |!

Details

❗ Test warnings:

pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/quantms/quantms/subworkflows/local/id/main.nf: _ ch_software_versions = ch_software_versions.mix(PHOSPHO_SCORING.out.versions.ifEmpty(null))
_
pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/quantms/quantms/subworkflows/local/dda_id/main.nf: _ ch_software_versions = ch_software_versions.mix(PHOSPHO_SCORING.out.versions.ifEmpty(null))
_

❔ Tests ignored:

files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: conf/test_full.config
files_exist - File is ignored: conf/test.config
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/awsfulltest.yml
files_exist - File is ignored: .github/workflows/ci.yml
files_exist - File is ignored: .github/workflows/download_pipeline.yml
files_exist - File is ignored: .github/workflows/nf-test.yml
files_exist - File is ignored: .gitignore
files_exist - File is ignored: conf/modules.config
files_exist - File is ignored: conf/igenomes_ignored.config
nextflow_config - nextflow_config
files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: docs/README.md
actions_nf_test - '.github/workflows/nf-test.yml' not found
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/quantms/quantms/.github/workflows/awstest.yml
multiqc_config - multiqc_config
modules_config - modules_config

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .nf-core.yml
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/CONTRIBUTING.md
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/actions/get-shards/action.yml
files_exist - File found: .github/actions/nf-test/action.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: assets/nf-core-quantms_logo_light.png
files_exist - File found: docs/images/nf-core-quantms_logo_light.png
files_exist - File found: docs/images/nf-core-quantms_logo_dark.png
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: nf-test.config
files_exist - File found: tests/default.nf.test
files_exist - File found: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: modules.json
files_exist - File found: ro-crate-metadata.json
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: docs/images/nf-core-quantms_logo.png
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowQuantms.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nf_test_content - 'tests/default.nf.test' contains outdir parameter
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/nextflow.config' contains modules_testdata_base_path
nf_test_content - 'tests/nextflow.config' contains pipelines_testdata_base_path
nf_test_content - 'nf-test.config' sets a testsDir
nf_test_content - 'nf-test.config' sets a workDir
nf_test_content - 'nf-test.config' sets a configFile
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - .github/workflows/linting.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
readme - README Nextflow minimum version badge matched config. Badge: 25.04.0, Config: 25.04.0
readme - README nf-core template version badge found.
readme - README Zenodo placeholder was replaced with DOI.
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (0 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: diann_private.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: extended_ci.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
local_component_structure - local subworkflows directory structure is correct 'subworkflows/local/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 3.5.2
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 3.5.2
Run at 2026-03-26 07:34:16

Initial plan

ec8103a

Copilot AI assigned Copilot and enryH Mar 25, 2026

Copilot started work on behalf of enryH March 25, 2026 20:41 View session

fix: correct typo inmermory -> inmemory in openms_peak_picker

0c46134

Co-authored-by: enryH <2833836+enryH@users.noreply.github.com> Agent-Logs-Url: https://github.com/bigbio/quantms/sessions/ef73a74e-d614-4f35-b4af-4c6994dd711d

Copilot AI changed the title ~~[WIP] Fix typo in openms_peak_picker documentation~~ Fix typo in openms_peak_picker processOption value Mar 25, 2026

Copilot AI requested a review from enryH March 25, 2026 20:43

Copilot finished work on behalf of enryH March 25, 2026 20:43

Merge branch 'dev' into copilot/fix-typo-in-openms-peak-picker

aaa0b91

enryH linked an issue Mar 26, 2026 that may be closed by this pull request

Typo in openms_peak_picker #688

Open

jpfeuffer marked this pull request as ready for review March 26, 2026 12:20

jpfeuffer approved these changes Mar 26, 2026

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Fix typo in openms_peak_picker processOption value#689

Fix typo in openms_peak_picker processOption value#689
Copilot wants to merge 3 commits intodevfrom
copilot/fix-typo-in-openms-peak-picker

Copilot AI commented Mar 25, 2026 •

edited

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github-actions bot commented Mar 26, 2026 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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Copilot AI commented Mar 25, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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Command used and terminal output

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github-actions bot commented Mar 26, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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Development

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Copilot AI commented Mar 25, 2026 •

edited

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github-actions bot commented Mar 26, 2026 •

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`nf-core pipelines lint` overall result: Passed ✅ ⚠️