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verified publisher icon nf-core

Update module: propr/propd

Open ninaxiong11 opened this issue 2 months ago • 2 comments

PR checklist

Update propr to 5.1.8 and limma to 3.62.1

  • [X] 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/differentialabundance branch on the nf-core/test-datasets repository.
  • [ ] Make sure your code lints (nf-core lint).
  • [ ] Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • [ ] Check for unexpected warnings in debug mode (nextflow run . -profile debug,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).

ninaxiong11 avatar Oct 29 '25 17:10 ninaxiong11

[!WARNING] Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.3.1. Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

nf-core-bot avatar Oct 29 '25 17:10 nf-core-bot

nf-core pipelines lint overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit 9ddd2e3

+| ✅ 389 tests passed       |+
#| ❔  10 tests were ignored |#
!| ❗  19 tests had warnings |!

:heavy_exclamation_mark: Test warnings:

  • 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 base.config: Check the defaults for all processes
  • 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!
  • schema_lint - Parameter input is not defined in the correct subschema (input_output_options)
  • schema_description - No description provided in schema for parameter: deseq2_seed
  • schema_description - No description provided in schema for parameter: dream_p_value
  • schema_description - No description provided in schema for parameter: dream_lfc
  • schema_description - No description provided in schema for parameter: dream_confint
  • schema_description - No description provided in schema for parameter: dream_proportion
  • schema_description - No description provided in schema for parameter: dream_stdev_coef_lim
  • schema_description - No description provided in schema for parameter: dream_trend
  • schema_description - No description provided in schema for parameter: dream_robust
  • schema_description - No description provided in schema for parameter: dream_winsor_tail_p
  • schema_description - No description provided in schema for parameter: dream_ddf
  • schema_description - No description provided in schema for parameter: dream_reml
  • schema_description - No description provided in schema for parameter: dream_apply_voom
  • schema_description - No description provided in schema for parameter: dream_adjust_method

:grey_question: Tests ignored:

  • files_exist - File is ignored: assets/multiqc_config.yml
  • nextflow_config - Config default ignored: params.report_file
  • nextflow_config - Config default ignored: params.logo_file
  • nextflow_config - Config default ignored: params.css_file
  • nextflow_config - Config default ignored: params.citations_file
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-differentialabundance_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-differentialabundance_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-differentialabundance_logo_dark.png
  • multiqc_config - multiqc_config

:white_check_mark: Tests passed:

  • files_exist - File found: .gitattributes
  • files_exist - File found: .gitignore
  • files_exist - File found: .nf-core.yml
  • 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/nf-test.yml
  • files_exist - File found: .github/actions/get-shards/action.yml
  • files_exist - File found: .github/actions/nf-test/action.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-differentialabundance_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-differentialabundance_logo_light.png
  • files_exist - File found: docs/images/nf-core-differentialabundance_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: nf-test.config
  • files_exist - File found: tests/default.nf.test
  • files_exist - File found: main.nf
  • files_exist - File found: conf/base.config
  • files_exist - File found: conf/igenomes.config
  • files_exist - File found: conf/igenomes_ignored.config
  • files_exist - File found: .github/workflows/awstest.yml
  • files_exist - File found: .github/workflows/awsfulltest.yml
  • 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-differentialabundance_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/WorkflowDifferentialabundance.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 - Found nf-schema plugin
  • 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: validation.help.enabled
  • 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 found: validation.help.beforeText
  • nextflow_config - Config variable found: validation.help.afterText
  • nextflow_config - Config variable found: validation.help.command
  • nextflow_config - Config variable found: validation.summary.beforeText
  • nextflow_config - Config variable found: validation.summary.afterText
  • 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 variable (correctly) not found: params.max_cpus
  • nextflow_config - Config variable (correctly) not found: params.max_memory
  • nextflow_config - Config variable (correctly) not found: params.max_time
  • nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
  • nextflow_config - Config variable (correctly) not found: params.validationLenientMode
  • nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
  • nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
  • 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: 1.6.0dev
  • 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.study_name= study
  • nextflow_config - Config default value correct: params.study_type= rnaseq
  • nextflow_config - Config default value correct: params.study_abundance_type= counts
  • nextflow_config - Config default value correct: params.round_digits= 4
  • nextflow_config - Config default value correct: params.observations_id_col= sample
  • nextflow_config - Config default value correct: params.observations_type= sample
  • nextflow_config - Config default value correct: params.features_id_col= gene_id
  • nextflow_config - Config default value correct: params.features_name_col= gene_name
  • nextflow_config - Config default value correct: params.features_type= gene
  • nextflow_config - Config default value correct: params.features_metadata_cols= gene_id,gene_name,gene_biotype
  • nextflow_config - Config default value correct: params.affy_file_name_col= file
  • nextflow_config - Config default value correct: params.affy_background= true
  • nextflow_config - Config default value correct: params.affy_bgversion= 2
  • nextflow_config - Config default value correct: params.affy_build_annotation= true
  • nextflow_config - Config default value correct: params.features_gtf_feature_type= transcript
  • nextflow_config - Config default value correct: params.features_gtf_table_first_field= gene_id
  • nextflow_config - Config default value correct: params.proteus_measurecol_prefix= LFQ intensity
  • nextflow_config - Config default value correct: params.proteus_norm_function= normalizeMedian
  • nextflow_config - Config default value correct: params.proteus_plotsd_method= violin
  • nextflow_config - Config default value correct: params.proteus_plotmv_loess= true
  • nextflow_config - Config default value correct: params.proteus_palette_name= Set1
  • nextflow_config - Config default value correct: params.filtering_min_abundance= 1.0
  • nextflow_config - Config default value correct: params.filtering_min_samples= 1.0
  • nextflow_config - Config default value correct: params.filtering_min_proportion_not_na= 0.5
  • nextflow_config - Config default value correct: params.immunedeconv_method= quantiseq
  • nextflow_config - Config default value correct: params.immunedeconv_function= deconvolute
  • nextflow_config - Config default value correct: params.exploratory_clustering_method= ward.D2
  • nextflow_config - Config default value correct: params.exploratory_cor_method= spearman
  • nextflow_config - Config default value correct: params.exploratory_n_features= 500
  • nextflow_config - Config default value correct: params.exploratory_whisker_distance= 1.5
  • nextflow_config - Config default value correct: params.exploratory_mad_threshold= -5
  • nextflow_config - Config default value correct: params.exploratory_main_variable= auto_pca
  • nextflow_config - Config default value correct: params.exploratory_assay_names= raw,normalised,variance_stabilised
  • nextflow_config - Config default value correct: params.exploratory_final_assay= variance_stabilised
  • nextflow_config - Config default value correct: params.exploratory_log2_assays= raw,normalised
  • nextflow_config - Config default value correct: params.exploratory_palette_name= Set1
  • nextflow_config - Config default value correct: params.differential_method= deseq2
  • nextflow_config - Config default value correct: params.differential_feature_id_column= gene_id
  • nextflow_config - Config default value correct: params.differential_fc_column= log2FoldChange
  • nextflow_config - Config default value correct: params.differential_pval_column= pvalue
  • nextflow_config - Config default value correct: params.differential_qval_column= padj
  • nextflow_config - Config default value correct: params.differential_min_fold_change= 2.0
  • nextflow_config - Config default value correct: params.differential_max_pval= 1.0
  • nextflow_config - Config default value correct: params.differential_max_qval= 0.05
  • nextflow_config - Config default value correct: params.differential_feature_name_column= gene_name
  • nextflow_config - Config default value correct: params.differential_foldchanges_logged= true
  • nextflow_config - Config default value correct: params.differential_palette_name= Set1
  • nextflow_config - Config default value correct: params.deseq2_test= Wald
  • nextflow_config - Config default value correct: params.deseq2_fit_type= parametric
  • nextflow_config - Config default value correct: params.deseq2_sf_type= ratio
  • nextflow_config - Config default value correct: params.deseq2_min_replicates_for_replace= 7
  • nextflow_config - Config default value correct: params.deseq2_independent_filtering= true
  • nextflow_config - Config default value correct: params.deseq2_lfc_threshold= 0
  • nextflow_config - Config default value correct: params.deseq2_alt_hypothesis= greaterAbs
  • nextflow_config - Config default value correct: params.deseq2_p_adjust_method= BH
  • nextflow_config - Config default value correct: params.deseq2_alpha= 0.1
  • nextflow_config - Config default value correct: params.deseq2_minmu= 0.5
  • nextflow_config - Config default value correct: params.deseq2_vs_method= vst
  • nextflow_config - Config default value correct: params.deseq2_shrink_lfc= true
  • nextflow_config - Config default value correct: params.deseq2_cores= 1
  • nextflow_config - Config default value correct: params.deseq2_vs_blind= true
  • nextflow_config - Config default value correct: params.deseq2_vst_nsub= 1000
  • nextflow_config - Config default value correct: params.limma_method= ls
  • nextflow_config - Config default value correct: params.limma_proportion= 0.01
  • nextflow_config - Config default value correct: params.limma_stdev_coef_lim= 0.1,4
  • nextflow_config - Config default value correct: params.limma_winsor_tail_p= 0.05,0.1
  • nextflow_config - Config default value correct: params.limma_lfc= 0
  • nextflow_config - Config default value correct: params.limma_adjust_method= BH
  • nextflow_config - Config default value correct: params.limma_p_value= 1.0
  • nextflow_config - Config default value correct: params.dream_p_value= 1
  • nextflow_config - Config default value correct: params.dream_lfc= 0
  • nextflow_config - Config default value correct: params.dream_proportion= 0.01
  • nextflow_config - Config default value correct: params.dream_stdev_coef_lim= 0.1,4
  • nextflow_config - Config default value correct: params.dream_winsor_tail_p= 0.05,0.1
  • nextflow_config - Config default value correct: params.dream_ddf= adaptive
  • nextflow_config - Config default value correct: params.dream_adjust_method= BH
  • nextflow_config - Config default value correct: params.gsea_permute= phenotype
  • nextflow_config - Config default value correct: params.gsea_nperm= 1000
  • nextflow_config - Config default value correct: params.gsea_scoring_scheme= weighted
  • nextflow_config - Config default value correct: params.gsea_metric= Signal2Noise
  • nextflow_config - Config default value correct: params.gsea_sort= real
  • nextflow_config - Config default value correct: params.gsea_order= descending
  • nextflow_config - Config default value correct: params.gsea_set_max= 500
  • nextflow_config - Config default value correct: params.gsea_set_min= 15
  • nextflow_config - Config default value correct: params.gsea_norm= meandiv
  • nextflow_config - Config default value correct: params.gsea_rnd_type= no_balance
  • nextflow_config - Config default value correct: params.gsea_make_sets= true
  • nextflow_config - Config default value correct: params.gsea_num= 100
  • nextflow_config - Config default value correct: params.gsea_plot_top_x= 20
  • nextflow_config - Config default value correct: params.gsea_rnd_seed= timestamp
  • nextflow_config - Config default value correct: params.gprofiler2_significant= true
  • nextflow_config - Config default value correct: params.gprofiler2_correction_method= gSCS
  • nextflow_config - Config default value correct: params.gprofiler2_max_qval= 0.05
  • nextflow_config - Config default value correct: params.gprofiler2_background_file= auto
  • nextflow_config - Config default value correct: params.gprofiler2_domain_scope= annotated
  • nextflow_config - Config default value correct: params.gprofiler2_min_diff= 1
  • nextflow_config - Config default value correct: params.gprofiler2_palette_name= Blues
  • nextflow_config - Config default value correct: params.decoupler_min_n= 5
  • nextflow_config - Config default value correct: params.decoupler_methods= ulm
  • nextflow_config - Config default value correct: params.shinyngs_build_app= true
  • nextflow_config - Config default value correct: params.report_scree= true
  • nextflow_config - Config default value correct: params.skip_reports= false
  • nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
  • 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.publish_dir_mode= copy
  • 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/
  • nf_test_content - 'tests/test_maxquant.nf.test' contains outdir parameter
  • nf_test_content - 'tests/test_maxquant.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_maxquant.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_maxquant.nf.test' contains outdir parameter
  • nf_test_content - 'tests/test_maxquant.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_maxquant.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_nogtf.nf.test' contains outdir parameter
  • nf_test_content - 'tests/test_nogtf.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_nogtf.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_nogtf.nf.test' contains outdir parameter
  • nf_test_content - 'tests/test_nogtf.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_nogtf.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/default.nf.test' contains outdir parameter
  • nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/default.nf.test' contains outdir parameter
  • nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/default.nf.test' contains outdir parameter
  • nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/default.nf.test' contains outdir parameter
  • nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/default.nf.test' contains outdir parameter
  • nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_affy.nf.test' contains outdir parameter
  • nf_test_content - 'tests/test_affy.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_affy.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_affy.nf.test' contains outdir parameter
  • nf_test_content - 'tests/test_affy.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_affy.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_rnaseq_limma.nf.test' contains outdir parameter
  • nf_test_content - 'tests/test_rnaseq_limma.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_rnaseq_limma.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_rnaseq_limma.nf.test' contains outdir parameter
  • nf_test_content - 'tests/test_rnaseq_limma.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_rnaseq_limma.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_rnaseq_limma.nf.test' contains outdir parameter
  • nf_test_content - 'tests/test_rnaseq_limma.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_rnaseq_limma.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_rnaseq_limma.nf.test' contains outdir parameter
  • nf_test_content - 'tests/test_rnaseq_limma.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_rnaseq_limma.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_rnaseq_dream.nf.test' contains outdir parameter
  • nf_test_content - 'tests/test_rnaseq_dream.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_rnaseq_dream.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_rnaseq_dream.nf.test' contains outdir parameter
  • nf_test_content - 'tests/test_rnaseq_dream.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_rnaseq_dream.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_rnaseq_dream.nf.test' contains outdir parameter
  • nf_test_content - 'tests/test_rnaseq_dream.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_rnaseq_dream.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_rnaseq_dream.nf.test' contains outdir parameter
  • nf_test_content - 'tests/test_rnaseq_dream.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_rnaseq_dream.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_custom_paramsheet.nf.test' contains outdir parameter
  • nf_test_content - 'tests/test_custom_paramsheet.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_custom_paramsheet.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_custom_paramsheet.nf.test' contains outdir parameter
  • nf_test_content - 'tests/test_custom_paramsheet.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_custom_paramsheet.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_custom_paramsheet.nf.test' contains outdir parameter
  • nf_test_content - 'tests/test_custom_paramsheet.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_custom_paramsheet.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_custom_paramsheet.nf.test' contains outdir parameter
  • nf_test_content - 'tests/test_custom_paramsheet.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_custom_paramsheet.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_soft.nf.test' contains outdir parameter
  • nf_test_content - 'tests/test_soft.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_soft.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_soft.nf.test' contains outdir parameter
  • nf_test_content - 'tests/test_soft.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/test_soft.nf.test' snapshots a 'versions.yml' file
  • nf_test_content - 'tests/nextflow.config' contains modules_testdata_base_path
  • nf_test_content - 'tests/nextflow.config' contains pipelines_testdata_base_path
  • nf_test_content - 'nf-test.config' sets a testsDir
  • nf_test_content - 'nf-test.config' sets a workDir
  • nf_test_content - 'nf-test.config' sets a configFile
  • 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/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 - docs/README.md matches the template
  • files_unchanged - .gitignore matches the template
  • files_unchanged - .prettierignore matches the template
  • actions_nf_test - '.github/workflows/nf-test.yml' is triggered on expected events
  • actions_nf_test - '.github/workflows/nf-test.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: 24.04.2, Config: 24.04.2
  • readme - README nf-core template version badge found.
  • readme - README Zenodo placeholder was replaced with DOI.
  • pipeline_if_empty_null - No ifEmpty(null) strings found
  • 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_params - Schema matched params returned from nextflow config
  • system_exit - No System.exit calls found
  • actions_schema_validation - Workflow validation passed: linting.yml
  • actions_schema_validation - Workflow validation passed: download_pipeline.yml
  • actions_schema_validation - Workflow validation passed: template-version-comment.yml
  • actions_schema_validation - Workflow validation passed: linting_comment.yml
  • actions_schema_validation - Workflow validation passed: release-announcements.yml
  • actions_schema_validation - Workflow validation passed: fix_linting.yml
  • actions_schema_validation - Workflow validation passed: nf-test.yml
  • actions_schema_validation - Workflow validation passed: awsfulltest.yml
  • actions_schema_validation - Workflow validation passed: branch.yml
  • actions_schema_validation - Workflow validation passed: awstest.yml
  • actions_schema_validation - Workflow validation passed: clean-up.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'
  • local_component_structure - local subworkflows directory structure is correct 'subworkflows/local/TOOL/SUBTOOL'
  • base_config - conf/base.config found and not ignored.
  • modules_config - conf/modules.config found and not ignored.
  • modules_config - GUNZIP_GTF found in conf/modules.config and Nextflow scripts.
  • modules_config - GTF_TO_TABLE found in conf/modules.config and Nextflow scripts.
  • modules_config - VALIDATOR found in conf/modules.config and Nextflow scripts.
  • modules_config - AFFY_JUSTRMA_RAW found in conf/modules.config and Nextflow scripts.
  • modules_config - AFFY_JUSTRMA_NORM found in conf/modules.config and Nextflow scripts.
  • modules_config - PROTEUS found in conf/modules.config and Nextflow scripts.
  • modules_config - GEOQUERY_GETGEO found in conf/modules.config and Nextflow scripts.
  • modules_config - CUSTOM_MATRIXFILTER found in conf/modules.config and Nextflow scripts.
  • modules_config - IMMUNEDECONV found in conf/modules.config and Nextflow scripts.
  • modules_config - DESEQ2_NORM found in conf/modules.config and Nextflow scripts.
  • modules_config - DESEQ2_DIFFERENTIAL found in conf/modules.config and Nextflow scripts.
  • modules_config - LIMMA_NORM found in conf/modules.config and Nextflow scripts.
  • modules_config - LIMMA_DIFFERENTIAL found in conf/modules.config and Nextflow scripts.
  • modules_config - VARIANCEPARTITION_DREAM found in conf/modules.config and Nextflow scripts.
  • modules_config - CUSTOM_FILTERDIFFERENTIALTABLE found in conf/modules.config and Nextflow scripts.
  • modules_config - CSVTK_JOIN found in conf/modules.config and Nextflow scripts.
  • modules_config - GSEA_GSEA found in conf/modules.config and Nextflow scripts.
  • modules_config - CUSTOM_TABULARTOGSEACLS found in conf/modules.config and Nextflow scripts.
  • modules_config - CUSTOM_TABULARTOGSEAGCT found in conf/modules.config and Nextflow scripts.
  • modules_config - CUSTOM_TABULARTOGSEACHIP found in conf/modules.config and Nextflow scripts.
  • modules_config - GPROFILER2_GOST found in conf/modules.config and Nextflow scripts.
  • modules_config - DECOUPLER_DECOUPLER found in conf/modules.config and Nextflow scripts.
  • modules_config - PLOT_EXPLORATORY found in conf/modules.config and Nextflow scripts.
  • modules_config - PLOT_DIFFERENTIAL found in conf/modules.config and Nextflow scripts.
  • modules_config - SHINYNGS_APP found in conf/modules.config and Nextflow scripts.
  • modules_config - QUARTONOTEBOOK found in conf/modules.config and Nextflow scripts.
  • modules_config - MAKE_REPORT_BUNDLE 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: 3.3.1
  • rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

  • nf-core/tools version 3.3.1
  • Run at 2025-10-29 17:08:02

github-actions[bot] avatar Oct 29 '25 17:10 github-actions[bot]

These changes are minimally disrupted, so I am gonna merge it.

suzannejin avatar Nov 20 '25 14:11 suzannejin