Release 2.4.1 #260

jonasscheid · 2023-04-04T13:55:49Z

`Added`

Added low resolution settings (e.g. Iontrap) #254 @steffenlem

`Fixed`

Increased comet search, through altering the spectrum_batch_size from 500 to 0
#249 - nf-core template update (version 2.7.2) @marissaDubbelaar
#258 - Adjusted decoy strategy to reverse #255 and made consistent fdr-level flags #228
#845 - Adjusted nf-core test data set #233

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 v2.7.2

…'null' folder creation and update the CHANGELOG

Prepare for 2.4.1 (patch)

Added low resolution settings to pipeline

Resolve Pythonblack issues

Adjust decoy strategy and fdr_level flag

github-actions · 2023-04-04T14:20:30Z

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

Posted for pipeline commit f7ddde2

+| ✅ 157 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

files_exist - File not found: conf/igenomes.config

✅ Tests passed:

files_exist - File found: .gitattributes
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files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
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files_exist - File found: lib/WorkflowMhcquant.groovy
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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
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nextflow_config - Config variable found: params.outdir
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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
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nextflow_config - Config variable (correctly) not found: params.nf_required_version
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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 manifest.version ends in dev: '2.4.1dev'
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
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files_unchanged - .gitignore matches the template
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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: 22.10.1, Config: 22.10.1
readme - README Nextflow minimum version in Quick Start section matched config. README: 22.10.1, Config: 22.10.1
pipeline_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (124 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: linting_comment.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: linting.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 2.7.2
Run at 2023-04-05 11:57:44

steffenlem

LGTM

bin/vcf_neoepitope_predictor.py

modules/local/openms_decoydatabase.nf

ramprasadn

LGTM! 👍🏻 🚀

FriederikeHanssen · 2023-04-06T08:59:37Z

nextflow.config

-    nextflowVersion = '!>=21.10.3'
-    version         = '2.3.2dev'
+    nextflowVersion = '!>=22.10.1'
+    version = '2.4.1dev'


dev needs to be removed before the release 🙈

FriederikeHanssen · 2023-04-06T09:00:15Z

CHANGELOG.md

@@ -3,6 +3,23 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

+## v2.4.1 nfcore/mhcquant "Maroon Gold Boxer" (patch) - 2023/04/04


the release date is not up-to-date anymore

FriederikeHanssen · 2023-04-06T09:02:50Z

Also just saw that in some places exit is still used. would be good to remove that and replace with Nextflow.error in the .groovy files and error in .nf files

jonasscheid and others added 30 commits November 22, 2022 16:22

Starting draft of bruker conversion feature

430255b

Template update for nf-core/tools version 2.7.1

83397b9

Template update for nf-core/tools version 2.7.2

9f38da6

Add more preliminary conversion code

ca22e29

Merge branch 'nf-core:dev' into dev

d200db7

Resolve conflicts and bump version

1ce08db

Make sure that the version number inlcudes dev

a1bfaf6

Add workable msconvert under docker

f6a54e5

sync with upstream branch

0ba19ae

Bump latest nextflow version to '22.10.1'

d2fa36e

Merge pull request #249 from nf-core/nf-core-template-merge-2.7.2

a58922c

Important! Template update for nf-core/tools v2.7.2

Alter the value of the spectrum_batch_size parameter, fix issue with …

7559a76

…'null' folder creation and update the CHANGELOG

Merge pull request #253 from marissaDubbelaar/master

9008c94

Prepare for 2.4.1 (patch)

Print warning when no peptides found instead of exiting

843781a

Changed data type for fragment_bin_offset to number

6aae4e9

Added instrument parameter

4f171f7

Added instrument adapter to modules config file

01940ec

Merge branch 'nf-core:dev' into dev

3a0289c

Merge pull request #254 from steffenlem/master

880fe41

Added low resolution settings to pipeline

Resolve black issues

264653b

Merge pull request #257 from marissaDubbelaar/master

20e2b00

Resolve Pythonblack issues

Merge branch 'nf-core:dev' into dev

8b4a0b1

Use no cleavage rule for decoy database generation

4cbd14b

change psm-level-fdrs to psm_level_fdrs

898bf40

Adjust changelog

f848c24

switch samplesheet for default test run

286c88c

add allelesheet in test config again

53a916f

Use new testdata

9e053c0

Adjust test configs

dda4941

run prettier

d4adcbb

jonasscheid and others added 2 commits April 4, 2023 11:47

changed date and added testdata fix to changelog

95c5d5b

Merge pull request #258 from jonasscheid/dev

5d4e49d

Adjust decoy strategy and fdr_level flag

steffenlem reviewed Apr 4, 2023

View reviewed changes

ramprasadn reviewed Apr 4, 2023

View reviewed changes

bin/vcf_neoepitope_predictor.py Show resolved Hide resolved

ramprasadn reviewed Apr 4, 2023

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modules/local/openms_decoydatabase.nf Show resolved Hide resolved

jonasscheid and others added 4 commits April 5, 2023 08:57

Add licenses to py files in bin

d6cc75a

Consistency in py files

dbf42e2

Updated authorships

95333e4

Merge pull request #262 from jonasscheid/dev

f7ddde2

ramprasadn approved these changes Apr 5, 2023

View reviewed changes

steffenlem approved these changes Apr 6, 2023

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jonasscheid merged commit 3feaf7c into master Apr 6, 2023

FriederikeHanssen reviewed Apr 6, 2023

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Release 2.4.1 #260

Release 2.4.1 #260

jonasscheid commented Apr 4, 2023 •

edited

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❗ Test warnings:

✅ Tests passed:

Run details

steffenlem left a comment

ramprasadn left a comment

FriederikeHanssen Apr 6, 2023

FriederikeHanssen Apr 6, 2023

FriederikeHanssen commented Apr 6, 2023

Release 2.4.1 #260

Release 2.4.1 #260

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jonasscheid commented Apr 4, 2023 • edited Loading

Added

Fixed

PR checklist

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

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

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FriederikeHanssen commented Apr 6, 2023

jonasscheid commented Apr 4, 2023 •

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`Added`

`Fixed`

github-actions bot commented Apr 4, 2023 •

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