quantms 0.0.10 -> 0.0.11 #419

ypriverol · 2024-09-10T06:35:48Z

PR checklist

Release of quantms v1.3.0

github-actions · 2024-09-10T06:37:20Z

`nf-core lint` overall result: Passed ✅

Posted for pipeline commit a426e07

+| ✅ 278 tests passed       |+
#| ❔  10 tests were ignored |#

❔ 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_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: .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: 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-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: modules.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
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 manifest.version ends in dev: 1.3.1dev
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
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.outdir= ./results
nextflow_config - Config default value correct: params.local_input_type= mzML
nextflow_config - Config default value correct: params.decoy_string= DECOY_
nextflow_config - Config default value correct: params.decoy_string_position= prefix
nextflow_config - Config default value correct: params.decoy_method= reverse
nextflow_config - Config default value correct: params.shuffle_max_attempts= 30
nextflow_config - Config default value correct: params.shuffle_sequence_identity_threshold= 0.5
nextflow_config - Config default value correct: params.decoydatabase_debug= 0
nextflow_config - Config default value correct: params.reindex_mzml= true
nextflow_config - Config default value correct: params.search_engines= comet
nextflow_config - Config default value correct: params.sage_processes= 1
nextflow_config - Config default value correct: params.enzyme= Trypsin
nextflow_config - Config default value correct: params.num_enzyme_termini= fully
nextflow_config - Config default value correct: params.allowed_missed_cleavages= 2
nextflow_config - Config default value correct: params.precursor_mass_tolerance= 5
nextflow_config - Config default value correct: params.precursor_mass_tolerance_unit= ppm
nextflow_config - Config default value correct: params.fragment_mass_tolerance= 0.03
nextflow_config - Config default value correct: params.fragment_mass_tolerance_unit= Da
nextflow_config - Config default value correct: params.fixed_mods= Carbamidomethyl (C)
nextflow_config - Config default value correct: params.variable_mods= Oxidation (M)
nextflow_config - Config default value correct: params.fragment_method= HCD
nextflow_config - Config default value correct: params.isotope_error_range= 0,1
nextflow_config - Config default value correct: params.protocol= automatic
nextflow_config - Config default value correct: params.min_precursor_charge= 2
nextflow_config - Config default value correct: params.max_precursor_charge= 4
nextflow_config - Config default value correct: params.min_peptide_length= 6
nextflow_config - Config default value correct: params.max_peptide_length= 40
nextflow_config - Config default value correct: params.num_hits= 1
nextflow_config - Config default value correct: params.max_mods= 3
nextflow_config - Config default value correct: params.min_peaks= 10
nextflow_config - Config default value correct: params.db_debug= 0
nextflow_config - Config default value correct: params.mod_localization= Phospho (S),Phospho (T),Phospho (Y)
nextflow_config - Config default value correct: params.unmatched_action= warn
nextflow_config - Config default value correct: params.IL_equivalent= true
nextflow_config - Config default value correct: params.skip_rescoring= false
nextflow_config - Config default value correct: params.ms2rescore= false
nextflow_config - Config default value correct: params.add_snr_feature_percolator= false
nextflow_config - Config default value correct: params.rescore_range= independent_run
nextflow_config - Config default value correct: params.ms2pip_model= HCD2021
nextflow_config - Config default value correct: params.feature_generators= deeplc,ms2pip
nextflow_config - Config default value correct: params.calibration_set_size= 0.15
nextflow_config - Config default value correct: params.posterior_probabilities= percolator
nextflow_config - Config default value correct: params.run_fdr_cutoff= 0.1
nextflow_config - Config default value correct: params.extractpsmfeature_debug= 0
nextflow_config - Config default value correct: params.idfilter_debug= 0
nextflow_config - Config default value correct: params.pp_debug= 0
nextflow_config - Config default value correct: params.idscoreswitcher_debug= 0
nextflow_config - Config default value correct: params.fdr_level= psm_level_fdrs
nextflow_config - Config default value correct: params.train_FDR= 0.05
nextflow_config - Config default value correct: params.test_FDR= 0.05
nextflow_config - Config default value correct: params.subset_max_train= 300000
nextflow_config - Config default value correct: params.percolator_debug= 0
nextflow_config - Config default value correct: params.outlier_handling= none
nextflow_config - Config default value correct: params.idpep_debug= 0
nextflow_config - Config default value correct: params.consensusid_algorithm= best
nextflow_config - Config default value correct: params.consensusid_debug= 0
nextflow_config - Config default value correct: params.reporter_mass_shift= 0.002
nextflow_config - Config default value correct: params.min_precursor_intensity= 1.0
nextflow_config - Config default value correct: params.min_precursor_purity= 0.0
nextflow_config - Config default value correct: params.min_reporter_intensity= 0.0
nextflow_config - Config default value correct: params.precursor_isotope_deviation= 10.0
nextflow_config - Config default value correct: params.isotope_correction= true
nextflow_config - Config default value correct: params.iso_normalization= false
nextflow_config - Config default value correct: params.reference_channel= 126
nextflow_config - Config default value correct: params.iso_debug= 0
nextflow_config - Config default value correct: params.idmapper_debug= 0
nextflow_config - Config default value correct: params.protein_inference_method= aggregation
nextflow_config - Config default value correct: params.protein_score= best
nextflow_config - Config default value correct: params.use_shared_peptides= true
nextflow_config - Config default value correct: params.min_peptides_per_protein= 1
nextflow_config - Config default value correct: params.top_PSMs= 1
nextflow_config - Config default value correct: params.update_PSM_probabilities= false
nextflow_config - Config default value correct: params.protein_level_fdr_cutoff= 0.01
nextflow_config - Config default value correct: params.picked_fdr= true
nextflow_config - Config default value correct: params.psm_level_fdr_cutoff= 0.01
nextflow_config - Config default value correct: params.protein_inference_debug= 0
nextflow_config - Config default value correct: params.top= 3
nextflow_config - Config default value correct: params.average= median
nextflow_config - Config default value correct: params.ratios= false
nextflow_config - Config default value correct: params.normalize= false
nextflow_config - Config default value correct: params.fix_peptides= false
nextflow_config - Config default value correct: params.include_all= true
nextflow_config - Config default value correct: params.protein_quant= unique_peptides
nextflow_config - Config default value correct: params.export_mztab= true
nextflow_config - Config default value correct: params.protein_quant_debug= 0
nextflow_config - Config default value correct: params.quantification_method= feature_intensity
nextflow_config - Config default value correct: params.targeted_only= true
nextflow_config - Config default value correct: params.feature_with_id_min_score= 0.1
nextflow_config - Config default value correct: params.feature_without_id_min_score= 0.75
nextflow_config - Config default value correct: params.lfq_intensity_threshold= 1000.0
nextflow_config - Config default value correct: params.alignment_order= star
nextflow_config - Config default value correct: params.quantify_decoys= false
nextflow_config - Config default value correct: params.plfq_debug= 0
nextflow_config - Config default value correct: params.mass_acc_automatic= true
nextflow_config - Config default value correct: params.scan_window_automatic= true
nextflow_config - Config default value correct: params.scan_window= 8
nextflow_config - Config default value correct: params.min_corr= 2.0
nextflow_config - Config default value correct: params.corr_diff= 1.0
nextflow_config - Config default value correct: params.time_corr_only= true
nextflow_config - Config default value correct: params.pg_level= 2.0
nextflow_config - Config default value correct: params.species_genes= false
nextflow_config - Config default value correct: params.skip_preliminary_analysis= false
nextflow_config - Config default value correct: params.diann_debug= 3
nextflow_config - Config default value correct: params.diann_normalize= true
nextflow_config - Config default value correct: params.random_preanalysis= false
nextflow_config - Config default value correct: params.random_preanalysis_seed= 42
nextflow_config - Config default value correct: params.empirical_assembly_ms_n= 200
nextflow_config - Config default value correct: params.msstats_threshold= 0.05
nextflow_config - Config default value correct: params.add_triqler_output= false
nextflow_config - Config default value correct: params.msstatslfq_feature_subset_protein= top3
nextflow_config - Config default value correct: params.msstatslfq_quant_summary_method= TMP
nextflow_config - Config default value correct: params.msstats_remove_one_feat_prot= true
nextflow_config - Config default value correct: params.msstatslfq_removeFewMeasurements= true
nextflow_config - Config default value correct: params.msstatsiso_useunique_peptide= true
nextflow_config - Config default value correct: params.msstatsiso_rmpsm_withfewmea_withinrun= true
nextflow_config - Config default value correct: params.msstatsiso_summaryformultiple_psm= sum
nextflow_config - Config default value correct: params.msstatsiso_summarization_method= msstats
nextflow_config - Config default value correct: params.msstatsiso_global_norm= true
nextflow_config - Config default value correct: params.msstatsiso_remove_norm_channel= true
nextflow_config - Config default value correct: params.msstatsiso_reference_normalization= true
nextflow_config - Config default value correct: params.msstats_plot_profile_qc= 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= 10d
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.skip_table_plots= false
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
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: 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 (225 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: branch.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting_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: 2.14.1

Run details

nf-core/tools version 2.14.1
Run at 2024-09-10 19:39:39

ypriverol · 2024-09-11T13:00:01Z

This major PR solves the following issue: #350

ypriverol added 4 commits August 29, 2024 09:45

Merge pull request #405 from bigbio/dev

48622b8

Release of quantms v1.3.0

quantms-utils 0.0.10 -> 0.0.11

f8fa8e3

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

0c0c811

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

195beaa

ypriverol added 5 commits September 10, 2024 07:54

actions/upload-artifact@v1 -> v2

9e42ec8

actions/upload-artifact@v2 -> v4

95b1cff

actions/upload-artifact@v2 -> v4

1b373be

actions/upload-artifact@v2 -> v4

912a545

actions/upload-artifact@v2 -> v4

a426e07

ypriverol linked an issue Sep 11, 2024 that may be closed by this pull request

USI reported by quantms for DIANN experiments. #350

Closed

3 tasks

ypriverol added the dia analysis label Sep 11, 2024

ypriverol merged commit 19450e3 into bigbio:dev Sep 11, 2024
17 checks passed

This was referenced Sep 11, 2024

USI reported by quantms for DIANN experiments. #350

Closed

ms2rescore.py arguments list #416

Closed

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quantms 0.0.10 -> 0.0.11 #419

quantms 0.0.10 -> 0.0.11 #419

ypriverol commented Sep 10, 2024

github-actions bot commented Sep 10, 2024 •

edited

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❔ Tests ignored:

✅ Tests passed:

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ypriverol commented Sep 11, 2024

quantms 0.0.10 -> 0.0.11 #419

quantms 0.0.10 -> 0.0.11 #419

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ypriverol commented Sep 10, 2024

PR checklist

github-actions bot commented Sep 10, 2024 • edited Loading

nf-core lint overall result: Passed ✅

❔ Tests ignored:

✅ Tests passed:

Run details

ypriverol commented Sep 11, 2024

github-actions bot commented Sep 10, 2024 •

edited

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`nf-core lint` overall result: Passed ✅