Release 2.5.0 #284

jonasscheid · 2023-10-04T07:23:53Z

Support for brukers tdf format by adding tdf2mzml converter #263
DeepLC retention time prediction
MS2PIP peak intensity prediction
Added OpenMS FileFilter to clean mzml after parsing to remove artifacts like empty spectra or precursors with charge 0 (optional)
Made file extension check case insensitive
Added option to provide a default comet parameters file
Optimize resource allocations
Update to latest template 2.10 #282
Restructured quantification to make use of enhanced rescoring:
Before

After

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/mhcquant branch on the nf-core/test-datasets repository.
Make sure your code lints (nf-core lint).
Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
Usage Documentation in docs/usage.md is updated.
Output Documentation in docs/output.md is updated.
CHANGELOG.md is updated.
README.md is updated (including new tool citations and authors/contributors).

Important! Template update for nf-core/tools v2.8

Update openms version

Add bruker file converter tdf2mzml

fix rawfileparser output bug

github-actions · 2023-10-04T07:26:31Z

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

Posted for pipeline commit 1990be7

+| ✅ 156 tests passed       |+
!| ❗   8 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 2.5.0
readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
pipeline_todos - TODO string in WorkflowMhcquant.groovy: Optionally add in-text citation tools to this list.
system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 51]
system_exit - System.exit in WorkflowMhcquant.groovy: System.exit(1) [line 18]
system_exit - System.exit in WorkflowMhcquant.groovy: System.exit(1) [line 45]
system_exit - System.exit in WorkflowMhcquant.groovy: System.exit(1) [line 51]

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
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: 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/ci.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-mhcquant_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-mhcquant_logo_light.png
files_exist - File found: docs/images/nf-core-mhcquant_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: lib/nfcore_external_java_deps.jar
files_exist - File found: lib/NfcoreTemplate.groovy
files_exist - File found: lib/Utils.groovy
files_exist - File found: lib/WorkflowMain.groovy
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.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: lib/WorkflowMhcquant.groovy
files_exist - File found: modules.json
files_exist - File found: pyproject.toml
files_exist - File not found check: Singularity
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: .nf-core.yaml
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: .github/workflows/push_dockerhub.yml
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: docs/images/nf-core-mhcquant_logo.png
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .yamllint.yml
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/Workflow.groovy
files_exist - File not found check: .travis.yml
nextflow_config - Config variable found: manifest.name
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: manifest.homePage
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: params.validationShowHiddenParams
nextflow_config - Config variable found: params.validationSchemaIgnoreParams
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
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/CONTRIBUTING.md 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/PULL_REQUEST_TEMPLATE.md 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-mhcquant_logo_light.png matches the template
files_unchanged - docs/images/nf-core-mhcquant_logo_light.png matches the template
files_unchanged - docs/images/nf-core-mhcquant_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - lib/nfcore_external_java_deps.jar matches the template
files_unchanged - lib/NfcoreTemplate.groovy matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
files_unchanged - pyproject.toml matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.yml' checks minimum NF version
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 23.04.0, Config: 23.04.0
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (137 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
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: release-announcments.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awstest.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
multiqc_config - 'assets/multiqc_config.yml' follows the ordering scheme of the minimally required plugins.
multiqc_config - 'assets/multiqc_config.yml' contains a matching 'report_comment'.
multiqc_config - 'assets/multiqc_config.yml' contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.10
Run at 2023-10-09 12:28:24

jonasscheid · 2023-10-04T07:28:05Z

test_quant and test_full run through locally. I need to adjust resource allocations / time limits. But first I want to gather the comments of reviews to bundle it

mapo9

Except for the minor cosmetic changes:
Great work, LGTM!

README.md

bin/check_samplesheet.py

subworkflows/local/quant.nf

workflows/mhcquant.nf

README.md

modules/local/tdf2mzml.nf

nextflow.config

Final changes for release 2.5.0

mapo9 · 2023-10-09T14:06:45Z

LGTM! 🚀

steffenlem

Looks good!

nf-core-bot and others added 30 commits April 28, 2023 14:24

Template update for nf-core/tools version 2.8

6151b2c

Resolve conflicts

e7695cb

resolve more conflicts

e586c40

fix linting

d7a1ccb

Merge pull request #264 from nf-core/nf-core-template-merge-2.8

9c1244f

Important! Template update for nf-core/tools v2.8

update openms version, rename parser

c78ad22

add skip_quantification to small test datase

e558b0e

adjust changelog

4889f37

Merge pull request #266 from jonasscheid/dev

60fc60a

Update openms version

Add bruker converter tdf2mzml

60b5456

fix linting

aa687e2

Merge pull request #267 from jonasscheid/dev

5bc762c

Add bruker file converter tdf2mzml

fix rawfileparser output bug

69d5875

Merge pull request #268 from jonasscheid/dev

58847d2

fix rawfileparser output bug

Added DeepLC script

97dd090

Call deeplc after comet

ea476f4

Changed input variable of DeepLC

b3e1d96

Added shebang to deeplc script

55a0f06

Adjusted paramter names for deeplc script

0598e6b

Fixed parameter name in deeplc script

d69ff73

Fix input/output parameter names

8e6ae4b

Added default error calculation

1bbecd9

Added deeplc features to percolator

f3fcdf7

Fixed deeplc output

c03395c

Updated schema with DeepLC parameters

32df09f

Updated changelog

296f96e

Linting

0a242fe

Fixed linting changes

ad407a5

Added newline at EOF

a1b0105

Fixed mail template

a7998db

jonasscheid and others added 10 commits October 2, 2023 23:21

limit cpus for ci

6baac65

spectrum batch size limit on ci tests to prevent crashing workflows

dd66c39

Update pyopenms to latest version in ionannotator

d59e1f4

increase speed of ci test

07b9713

typo

86c740c

remove unused dependency

3b0d487

speed up ci quant and fulltest

758e8f2

Add comments to subworkflows

cff9bc9

update changelog

d59d2e5

Merge pull request #280 from jonasscheid/rearrange_quant

87141eb

mapo9 requested changes Oct 4, 2023

View reviewed changes

steffenlem reviewed Oct 5, 2023

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README.md Outdated Show resolved Hide resolved

steffenlem requested changes Oct 6, 2023

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jonasscheid and others added 11 commits October 7, 2023 21:42

incorporate feedback

f76dd19

Movve quant test to test full bc of github limitations

6877012

move quant test solely to test_full

f76fb7f

update warning for refine fdr

2bf573d

prettier

090aaa3

remove deeplc and ms2pip from test_full since test stops bc of runtime

0d0f46b

reduce test_full bc no more storage of device (github)

6d11bcc

remove class1 and class2 from test_full

db8ad1d

only use quant in test_full due to space issue on gh

9f10857

feedback

eb6d692

Merge pull request #285 from jonasscheid/rearrange_quant

1990be7

Final changes for release 2.5.0

mapo9 approved these changes Oct 9, 2023

View reviewed changes

steffenlem approved these changes Oct 10, 2023

View reviewed changes

jonasscheid merged commit b80a5a4 into master Oct 10, 2023
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Release 2.5.0 #284

Release 2.5.0 #284

jonasscheid commented Oct 4, 2023 •

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github-actions bot commented Oct 4, 2023 •

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❗ Test warnings:

✅ Tests passed:

Run details

jonasscheid commented Oct 4, 2023

mapo9 left a comment •

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mapo9 commented Oct 9, 2023

steffenlem left a comment

Release 2.5.0 #284

Release 2.5.0 #284

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jonasscheid commented Oct 4, 2023 • edited Loading

PR checklist

github-actions bot commented Oct 4, 2023 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

Run details

jonasscheid commented Oct 4, 2023

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jonasscheid commented Oct 4, 2023 •

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

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