Fixing quantms rescoring bugs #462

ypriverol · 2024-12-19T17:09:15Z

This PR fixes the following Bug #458

PR checklist

coderabbitai · 2024-12-19T17:09:24Z

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github-actions · 2024-12-19T17:10:47Z

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

Posted for pipeline commit e6a811c

+| ✅ 109 tests passed       |+
#| ❔  13 tests were ignored |#
!| ❗  13 tests had warnings |!

❗ Test warnings:

pipeline_todos - TODO string in ro-crate-metadata.json: "description": "
\n \n <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-quantms_logo_dark.png">\n <img alt="nf-core/quantms" src="docs/images/nf-core-quantms_logo_light.png">\n \n
\n\n\n \n\n\n\n\n\n\n\n\n \n\n## Introduction\n\nnf-core/quantms is a bioinformatics pipeline that ...\n\n TODO nf-core:\n Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n major pipeline sections and the types of output it produces. You're giving an overview to someone new\n to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n\n\n Include a figure that guides the user through the major workflow steps. Many nf-core\n workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples. \n Fill in short bullet-pointed list of the default steps in the pipeline \n\n1. Read QC (FastQC)\n2. Present QC for raw reads (MultiQC)\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.\n\n Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\nsamplesheet.csv:\n\ncsv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n\n\nNow, you can run the pipeline using:\n\n update the following command to include all required parameters for a minimal example \n\nbash\nnextflow run nf-core/quantms \\\n -profile <docker/singularity/.../institute> \\\n --input samplesheet.csv \\\n --outdir <OUTDIR>\n\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.\n\nFor more details and further functionality, please refer to the usage documentation and the parameter documentation.\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\noutput documentation.\n\n## Credits\n\nnf-core/quantms was originally written by Yasset Perez-Riverol.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n If applicable, make list of people who have also contributed \n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the contributing guidelines.\n\nFor further information or help, don't hesitate to get in touch on the Slack #quantms channel (you can join with this invite).\n\n## Citations\n\n Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. \n If you use nf-core/quantms for your analysis, please cite it using the following doi: 10.5281/zenodo.XXXXXX \n\n Add bibliography of tools and data used in your pipeline \n\nAn extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.\n\nYou can cite the nf-core publication as follows:\n\n> The nf-core framework for community-curated bioinformatics pipelines.\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.\n",
pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
pipeline_todos - TODO string in base.config: Check the defaults for all processes
pipeline_todos - TODO string in base.config: Customise requirements for specific processes.

❔ 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: .gitignore
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_awstest - 'awstest.yml' workflow not found: /home/runner/work/quantms/quantms/.github/workflows/awstest.yml
multiqc_config - multiqc_config

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .nf-core.yml
files_exist - File found: .editorconfig
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/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: conf/modules.config
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: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: conf/igenomes_ignored.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
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md 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/config.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 - assets/nf-core-quantms_logo_light.png matches the template
files_unchanged - docs/images/nf-core-quantms_logo_light.png matches the template
files_unchanged - docs/images/nf-core-quantms_logo_dark.png matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.yml' checks minimum NF version
readme - README Nextflow minimum version badge matched config. Badge: 24.04.2, Config: 24.04.2
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/tsv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: diann_private.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: template_version_comment.yml
actions_schema_validation - Workflow validation passed: ci.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'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - NFCORE_QUANTMS found in conf/modules.config and Nextflow scripts.
modules_config - NFCORE_QUANTMS found in conf/modules.config and Nextflow scripts.
modules_config - MS2RESCORE found in conf/modules.config and Nextflow scripts.
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: 3.1.0

Run details

nf-core/tools version 3.1.0
Run at 2024-12-20 12:51:32

jpfeuffer · 2024-12-19T18:47:54Z

Could you please describe the bug in summary and how your changes fix that?

ypriverol · 2024-12-19T19:01:09Z

Could you please describe the bug in summary and how your changes fix that?

For MSGF+ but also any other search engines, the rescoring algorithm was failing for psms without a main score. #.

In the current PR, @daichengxin https://github.com/bigbio/quantms-rescoring/pull/5/files#diff-d6a7c234404ec9682d47dca3803cc1755e81134d9f19b11b97264f46cf339296R254 is now handling better.

jpfeuffer · 2024-12-19T19:02:43Z

How can a PeptideHit not have a main score?
This is impossible in idXML.

daichengxin · 2024-12-20T07:45:23Z

Normal peptidehit:

		<PeptideIdentification score_type="SpecEValue" higher_score_better="false" significance_threshold="0.0" MZ="454.995086669921875" RT="631.48025999999993" spectrum_reference="controllerType=0 controllerNumber=1 scan=2402" >
			<PeptideHit score="5.606986999999999e-08" sequence=".(TMT6plex)AERALTM(Oxidation)YM(Oxidation)LK(TMT6plex)" charge="4" aa_before="K" aa_after="N" start="2366" end="2376" protein_refs="PH_2117" >
				<UserParam type="int" name="MS:1002049" value="58"/>
				<UserParam type="int" name="MS:1002050" value="133"/>
				<UserParam type="float" name="MS:1002052" value="5.606986999999999e-08"/>
				<UserParam type="float" name="MS:1002053" value="2.466499"/>
				<UserParam type="string" name="AssumedDissociationMethod" value="CID"/>
				<UserParam type="string" name="CTermIonCurrentRatio" value="0.5432841"/>
				<UserParam type="string" name="ExplainedIonCurrentRatio" value="0.64345765"/>
				<UserParam type="string" name="MS2IonCurrent" value="398487.38"/>
				<UserParam type="string" name="MeanErrorAll" value="264.05197"/>
				<UserParam type="string" name="MeanErrorTop7" value="312.92484"/>
				<UserParam type="string" name="MeanRelErrorAll" value="173.04474"/>
				<UserParam type="string" name="MeanRelErrorTop7" value="234.3867"/>
				<UserParam type="string" name="NTermIonCurrentRatio" value="0.100173555"/>
				<UserParam type="string" name="NumMatchedMainIons" value="9"/>
				<UserParam type="string" name="StdevErrorAll" value="277.724"/>
				<UserParam type="string" name="StdevErrorTop7" value="296.51938"/>
				<UserParam type="string" name="StdevRelErrorAll" value="341.92044"/>
				<UserParam type="string" name="StdevRelErrorTop7" value="361.8129"/>
				<UserParam type="float" name="calcMZ" value="455.007080078125"/>
				<UserParam type="int" name="pass_threshold" value="1"/>
				<UserParam type="int" name="start" value="2367"/>
				<UserParam type="int" name="end" value="2377"/>
				<UserParam type="string" name="target_decoy" value="decoy"/>
				<UserParam type="string" name="isotope_error" value="0"/>
				<UserParam type="string" name="protein_references" value="unique"/>
				<UserParam type="float" name="MSGF:ScoreRatio" value="0.43609022556391"/>
				<UserParam type="float" name="MSGF:Energy" value="75.0"/>
				<UserParam type="float" name="MSGF:lnEValue" value="-0.902799736258774"/>
				<UserParam type="float" name="MSGF:lnExplainedIonCurrentRatio" value="-0.44074366776915"/>
				<UserParam type="float" name="MSGF:lnNTermIonCurrentRatio" value="-2.299853277801329"/>
				<UserParam type="float" name="MSGF:lnCTermIonCurrentRatio" value="-0.609938842631449"/>
				<UserParam type="float" name="MSGF:lnMS2IonCurrent" value="12.895431107953099"/>
				<UserParam type="float" name="MSGF:MeanErrorTop7" value="312.924840000000017"/>
				<UserParam type="float" name="MSGF:sqMeanErrorTop7" value="9.79219554890256e04"/>
				<UserParam type="float" name="MSGF:StdevErrorTop7" value="296.519380000000012"/>
			</PeptideHit>
			<UserParam type="string" name="MS:1001115" value="2402"/>
		</PeptideIdentification>

A error example without search engines score features, and NumMatchedMainIons is 0. So we should remove it or we will get an error from ms2rescore hander. I added a patch hander to skip them when extracting PSM. But I forget to synchronise the deletion of peptide ids. So in this commit I synchronised the deletion of the peptides

		<PeptideHit score="5.607171999999999e-08" sequence=".(TMT6plex)WGFAK(TMT6plex)VQK(TMT6plex)" charge="3" aa_before="R" aa_after="I" start="335" end="342" protein_refs="PH_6493" >
				<UserParam type="int" name="MS:1002049" value="-6"/>
				<UserParam type="int" name="MS:1002050" value="17"/>
				<UserParam type="float" name="MS:1002052" value="5.607171999999999e-08"/>
				<UserParam type="float" name="MS:1002053" value="2.4330258"/>
				<UserParam type="string" name="AssumedDissociationMethod" value="HCD"/>
				<UserParam type="string" name="CTermIonCurrentRatio" value="0.0"/>
				<UserParam type="string" name="ExplainedIonCurrentRatio" value="0.0"/>
				<UserParam type="string" name="MS2IonCurrent" value="349679.66"/>
				<UserParam type="float" name="MeanErrorAll" value="0.0"/>
				<UserParam type="float" name="MeanErrorTop7" value="0.0"/>
				<UserParam type="float" name="MeanRelErrorAll" value="0.0"/>
				<UserParam type="float" name="MeanRelErrorTop7" value="0.0"/>
				<UserParam type="string" name="NTermIonCurrentRatio" value="0.0"/>
				<UserParam type="int" name="NumMatchedMainIons" value="0"/>
				<UserParam type="float" name="StdevErrorAll" value="0.0"/>
				<UserParam type="float" name="StdevErrorTop7" value="0.0"/>
				<UserParam type="float" name="StdevRelErrorAll" value="0.0"/>
				<UserParam type="float" name="StdevRelErrorTop7" value="0.0"/>
				<UserParam type="float" name="calcMZ" value="551.0147705078125"/>
				<UserParam type="int" name="pass_threshold" value="1"/>
				<UserParam type="int" name="start" value="336"/>
				<UserParam type="int" name="end" value="343"/>
				<UserParam type="string" name="target_decoy" value="decoy"/>
				<UserParam type="string" name="isotope_error" value="1"/>
				<UserParam type="string" name="protein_references" value="unique"/>
			</PeptideHit>

jpfeuffer · 2024-12-20T08:23:15Z

Aha! That makes sense!

# Conflicts: # .github/workflows/awsfulltest.yml # .github/workflows/release-announcements.yml # .nf-core.yml # conf/modules.config # docs/usage.md # modules.json # modules/nf-core/fastqc/main.nf # modules/nf-core/fastqc/meta.yml # nextflow.config

ypriverol added 2 commits December 19, 2024 17:07

rescoring 0.0.1 -> 0.0.2

992981c

Merge branch 'dev' of https://github.com/bigbio/quantms into dev

41e66d9

ypriverol requested a review from daichengxin December 19, 2024 17:09

ypriverol added 11 commits December 20, 2024 09:59

Improved the .gitignore

a9b3c52

Template update for nf-core/tools version 3.0.2

e0d9e46

Merge branch 'TEMPLATE' into dev

8a70cdc

update template.

3d548c8

Template update for nf-core/tools version 3.1.0

c2ab929

Merge branch 'TEMPLATE' into dev

098c783

# Conflicts: # .github/workflows/awsfulltest.yml # .github/workflows/release-announcements.yml # .nf-core.yml # conf/modules.config # docs/usage.md # modules.json # modules/nf-core/fastqc/main.nf # modules/nf-core/fastqc/meta.yml # nextflow.config

update template.

88e6e2b

update template.

6ff5cd0

update template.

4def861

update template 3.1.0

203cd97

Merge remote-tracking branch 'origin/dev' into dev

e1b13d8

ypriverol linked an issue Dec 20, 2024 that may be closed by this pull request

Another error of quantms ms2rescore and OpenMS #458

Closed

update template 3.1.0

e6a811c

ypriverol requested a review from jpfeuffer December 20, 2024 14:39

daichengxin approved these changes Dec 20, 2024

View reviewed changes

ypriverol merged commit c6e862a into bigbio:dev Dec 20, 2024
21 checks passed

ypriverol mentioned this pull request Dec 20, 2024

Another error of quantms ms2rescore and OpenMS #458

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Fixing quantms rescoring bugs #462

Fixing quantms rescoring bugs #462

ypriverol commented Dec 19, 2024

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❗ Test warnings:

\n \n <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-quantms_logo_dark.png">\n <img alt="nf-core/quantms" src="docs/images/nf-core-quantms_logo_light.png">\n \n

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✅ Tests passed:

Run details

jpfeuffer commented Dec 19, 2024

ypriverol commented Dec 19, 2024

jpfeuffer commented Dec 19, 2024

daichengxin commented Dec 20, 2024 •

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jpfeuffer commented Dec 20, 2024

Fixing quantms rescoring bugs #462

Fixing quantms rescoring bugs #462

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ypriverol commented Dec 19, 2024

PR checklist

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CodeRabbit Configuration File (.coderabbit.yaml)

Documentation and Community

github-actions bot commented Dec 19, 2024 • edited Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

\n \n <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-quantms_logo_dark.png">\n <img alt="nf-core/quantms" src="docs/images/nf-core-quantms_logo_light.png">\n \n

❔ Tests ignored:

✅ Tests passed:

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jpfeuffer commented Dec 19, 2024

ypriverol commented Dec 19, 2024

jpfeuffer commented Dec 19, 2024

daichengxin commented Dec 20, 2024 • edited Loading

jpfeuffer commented Dec 20, 2024

coderabbitai bot commented Dec 19, 2024 •

edited

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CodeRabbit Configuration File (`.coderabbit.yaml`)

github-actions bot commented Dec 19, 2024 •

edited

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

daichengxin commented Dec 20, 2024 •

edited

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