Release 2.6.0

[jonasscheid]

Highlights

Added

• Added MS²Rescore module with the underlying python CLI #293 🤖
• Added support for handling various archive formats: d|d.tar.gz|d.tar|d.zip|mzML.gz|raw|RAW|mzML #323
  --> Provide PRIDE ftp link of raw data in samplesheet to directly stage + process projects 🥳

Fixed

• Create only one decoy database #299 🚀
• Use groupKey to streamline group-wise processing #310 🚀
• Replaced local modules with nf-core modules #310 🍏

Comments

• --use_deeplc and --use_ms2pip were removed and can now be specified via --feature_generators deeplc,ms2pip
• --ms2pip_model_name was renamed to --ms2pip_model

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).

[github-actions]

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 722343b

+| ✅ 234 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

• nextflow_config - Config manifest.version should end in dev: 2.6.0

❔ Tests ignored:

• files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md

✅ Tests passed:

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• 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
• nextflow_config - nextflow.config contains configuration profile test
• nextflow_config - Config default value correct: params.run_centroidisation= false
• nextflow_config - Config default value correct: params.pick_ms_levels= 2
• nextflow_config - Config default value correct: params.filter_mzml= false
• nextflow_config - Config default value correct: params.instrument= high_res
• nextflow_config - Config default value correct: params.enzyme= unspecific cleavage
• nextflow_config - Config default value correct: params.activation_method= ALL
• nextflow_config - Config default value correct: params.precursor_mass_tolerance= 5
• nextflow_config - Config default value correct: params.precursor_error_units= ppm
• nextflow_config - Config default value correct: params.fragment_bin_offset= 0.0
• nextflow_config - Config default value correct: params.fragment_mass_tolerance= 0.01
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• nextflow_config - Config default value correct: params.variable_mods= Oxidation (M)
• nextflow_config - Config default value correct: params.num_hits= 1
• nextflow_config - Config default value correct: params.remove_precursor_peak= false
• nextflow_config - Config default value correct: params.spectrum_batch_size= 0
• nextflow_config - Config default value correct: params.rescoring_engine= percolator
• nextflow_config - Config default value correct: params.feature_generators= deeplc,ms2pip
• nextflow_config - Config default value correct: params.ms2pip_model= Immuno-HCD
• nextflow_config - Config default value correct: params.deeplc_calibration_set_size= 0.15
• nextflow_config - Config default value correct: params.fdr_level= peptide_level_fdrs
• nextflow_config - Config default value correct: params.fdr_threshold= 0.01
• nextflow_config - Config default value correct: params.subset_max_train= 0
• nextflow_config - Config default value correct: params.quantify= false
• nextflow_config - Config default value correct: params.max_rt_alignment_shift= 300
• nextflow_config - Config default value correct: params.quantification_min_prob= 0.0
• nextflow_config - Config default value correct: params.quantification_mz_window= 5.0
• nextflow_config - Config default value correct: params.quantification_rt_window= 0.0
• nextflow_config - Config default value correct: params.quantification_mapping_tolerance= 0.0
• nextflow_config - Config default value correct: params.quantification_peak_width= 60.0
• nextflow_config - Config default value correct: params.quantification_min_peak_width= 0.2
• nextflow_config - Config default value correct: params.peptide_min_length= 8
• nextflow_config - Config default value correct: params.peptide_max_length= 12
• nextflow_config - Config default value correct: params.annotate_ions= false
• nextflow_config - Config default value correct: params.custom_config_version= master
• nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
• nextflow_config - Config default value correct: params.max_cpus= 16
• nextflow_config - Config default value correct: params.max_memory= 128.GB
• nextflow_config - Config default value correct: params.max_time= 240.h
• nextflow_config - Config default value correct: params.publish_dir_mode= copy
• nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
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• 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
• readme - README Zenodo placeholder was replaced with DOI.
• pipeline_todos - No TODO strings found
• pipeline_name_conventions - Name adheres to nf-core convention
• template_strings - Did not find any Jinja template strings (167 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: ci.yml
• actions_schema_validation - Workflow validation passed: awsfulltest.yml
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• 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 found and not ignored.
• multiqc_config - assets/multiqc_config.yml contains report_section_order
• multiqc_config - assets/multiqc_config.yml contains export_plots
• multiqc_config - assets/multiqc_config.yml contains report_comment
• 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'
• base_config - conf/base.config found and not ignored.
• base_config - TDF2MZML found in conf/base.config and Nextflow scripts.
• modules_config - conf/modules.config found and not ignored.
• modules_config - THERMORAWFILEPARSER found in conf/modules.config and Nextflow scripts.
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• modules_config - UNZIP found in conf/modules.config and Nextflow scripts.
• modules_config - GUNZIP found in conf/modules.config and Nextflow scripts.
• modules_config - OPENMS_DECOYDATABASE found in conf/modules.config and Nextflow scripts.
• modules_config - OPENMS_PEAKPICKERHIRES found in conf/modules.config and Nextflow scripts.
• modules_config - OPENMS_IDMERGER found in conf/modules.config and Nextflow scripts.
• modules_config - OPENMS_IDFILTER_Q_VALUE found in conf/modules.config and Nextflow scripts.
• modules_config - OPENMS_IDFILTER_QUANT found in conf/modules.config and Nextflow scripts.
• modules_config - OPENMS_IDRIPPER found in conf/modules.config and Nextflow scripts.
• modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_MHCQUANT found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_MHCQUANT found in conf/modules.config and Nextflow scripts.
• modules_config - TDF2MZML found in conf/modules.config and Nextflow scripts.
• modules_config - OPENMS_FILEFILTER found in conf/modules.config and Nextflow scripts.
• modules_config - OPENMS_MAPALIGNERIDENTIFICATION found in conf/modules.config and Nextflow scripts.
• modules_config - OPENMS_MAPRTTRANSFORMERMZML found in conf/modules.config and Nextflow scripts.
• modules_config - OPENMS_COMETADAPTER found in conf/modules.config and Nextflow scripts.
• modules_config - OPENMS_PEPTIDEINDEXER found in conf/modules.config and Nextflow scripts.
• modules_config - MS2RESCORE found in conf/modules.config and Nextflow scripts.
• modules_config - OPENMS_PERCOLATORADAPTER found in conf/modules.config and Nextflow scripts.
• modules_config - OPENMS_PSMFEATUREEXTRACTOR found in conf/modules.config and Nextflow scripts.
• modules_config - OPENMS_MZTABEXPORTER found in conf/modules.config and Nextflow scripts.
• modules_config - OPENMS_FEATUREFINDERIDENTIFICATION found in conf/modules.config and Nextflow scripts.
• modules_config - OPENMS_FEATURELINKERUNLABELEDKD found in conf/modules.config and Nextflow scripts.
• modules_config - OPENMS_TEXTEXPORTER found in conf/modules.config and Nextflow scripts.
• modules_config - OPENMS_IDCONFLICTRESOLVER found in conf/modules.config and Nextflow scripts.
• modules_config - PYOPENMS_IONANNOTATOR 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: 2.14.1

Run details

• nf-core/tools version 2.14.1
• Run at 2024-06-17 11:40:28

[marissaDubbelaar]

A lot of effort went into this PR!
On a small note, I would change the version to 2.0 since many changes were made, and the prediction of classes and rt is retired at the moment.
Maybe someone from the core team or contributors can give a second review.

[mirpedrol]

LGTM!
I only commented a couple of small details.
It's great that you could change some of the local modules for nf-core modules :) But I am wondering if the remaining local modules such as all the openms tools could also be nf-core modules? note that you can use nf-core modules patch if you need to make small modifications to the module. Anyway, I don't want this to be a blocker for this PR, just something to consider after release.

[jonasscheid]

Thanks for the reviews!