Nf core template update 3.3.1 by SusiJo · Pull Request #468 · nf-core/differentialabundance

SusiJo · 2025-06-04T12:35:05Z

PR checklist

…nto nf-core-template-update-3.3.1

github-actions · 2025-06-04T12:36:59Z

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

Posted for pipeline commit bb1a6ad

+| ✅ 356 tests passed       |+
#| ❔  10 tests were ignored |#
!| ❗   6 tests had warnings |!

Details

❗ 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 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!
pipeline_todos - TODO string in base.config: Check the defaults for all processes
schema_lint - Parameter input is not defined in the correct subschema (input_output_options)

❔ 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

✅ 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.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.shinyngs_build_app= true
nextflow_config - Config default value correct: params.report_scree= true
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_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_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_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_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_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/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_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/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/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: fix_linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: template-version-comment.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 - 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 - 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 - RMARKDOWNNOTEBOOK 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 2025-06-23 07:07:39

mirpedrol · 2025-06-04T15:02:26Z

@nf-core-bot fix linting please!

mashehu · 2025-06-11T11:31:18Z

yay, new linting error!

SusiJo · 2025-06-11T11:42:04Z

Thanks for helping with the linting @mashehu!
This new error is interesting though because locally I just get 1 failed test and not 3. Locally it does not complain about the logos in assets.

mashehu · 2025-06-11T12:21:12Z

The logos is a common one, which is not easy to fix on the tools side. Easiest is to add them to the point ignore list

famosab · 2025-06-13T08:12:20Z

@mashehu I added the fix to the nf-test action that you suggested but it seems like no difference is shown on the CI runs :(

…ferentialabundance into nf-core-template-update-3.3.1

mashehu · 2025-06-16T07:20:13Z

@mashehu I added the fix to the nf-test action that you suggested but it seems like no difference is shown on the CI runs :(

this is weird, they variable is still set in the actual workflow file 🤔 https://github.com/nf-core/differentialabundance/actions/runs/15636946038/workflow#L102-L103

mashehu · 2025-06-16T07:22:48Z

ah, found where they are coming from 6e5add5
should be fine now.

famosab

Removing some empty lines and wondering why there are a few of the snapshots with huge changes :) other than that it looks good!

famosab

LGTM

nf-core-bot and others added 2 commits June 3, 2025 11:01

Template update for nf-core/tools version 3.3.1

64ee28a

Merge branch 'TEMPLATE' of github.com:nf-core/differentialabundance i…

098af13

…nto nf-core-template-update-3.3.1

SusiJo added 4 commits June 4, 2025 14:55

update test affy

f39056a

fix lint

8f6dc5b

fix linting

608ceeb

update snapshot affy

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[automated] Fix code linting

90af2cd

mashehu reviewed Jun 11, 2025

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Comment thread modules.json

SusiJo added 3 commits June 11, 2025 13:11

update modules.json

8dcbb49

fix linting

216b8bf

trim whitespace

ad0ec2a

mashehu reviewed Jun 11, 2025

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Comment thread modules.json Outdated

update modules.json

5d6b2b2

SusiJo added 2 commits June 11, 2025 15:25

fix linting

5dd2e96

rm whitespace

6e45682

SusiJo force-pushed the nf-core-template-update-3.3.1 branch from 385ba8f to 6e45682 Compare June 11, 2025 13:32

update tests

3aaf840

SusiJo force-pushed the nf-core-template-update-3.3.1 branch from 9fa6a00 to 3aaf840 Compare June 12, 2025 13:30

famosab reviewed Jun 12, 2025

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Comment thread tests/default.nf.test.snap Outdated

famosab reviewed Jun 13, 2025

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Comment thread .github/actions/nf-test/action.yml Outdated

Update .github/actions/nf-test/action.yml

802de13

SusiJo added 3 commits June 13, 2025 11:20

add limits

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Merge branch 'nf-core-template-update-3.3.1' of github.com:SusiJo/dif…

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…ferentialabundance into nf-core-template-update-3.3.1

update snapshot default test

45bd353

famosab reviewed Jun 16, 2025

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Comment thread tests/.nftignore

update default test

da89eaf

SusiJo force-pushed the nf-core-template-update-3.3.1 branch from 6e5add5 to da89eaf Compare June 16, 2025 10:43

SusiJo added 2 commits June 16, 2025 12:55

ignore other tests

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update

a85802d

famosab reviewed Jun 16, 2025

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Comment thread tests/.nftignore

SusiJo and others added 4 commits June 16, 2025 12:24

test from codespaces

a082939

pre-commit

210c621

rm md5 rds

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update test_affy

6220a67

mashehu reviewed Jun 17, 2025

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Comment thread .github/workflows/nf-test.yml Outdated

SusiJo force-pushed the nf-core-template-update-3.3.1 branch from a6eeca6 to ab72190 Compare June 17, 2025 07:03

apply suggestions

da509a4

SusiJo force-pushed the nf-core-template-update-3.3.1 branch from ab72190 to da509a4 Compare June 17, 2025 07:48

mashehu reviewed Jun 17, 2025

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Comment thread nf-test.config

Comment thread nf-test.config Outdated

Comment thread tests/test_maxquant.nf.test.bak Outdated

Comment thread tests/test_nogtf.nf.test.bak Outdated

SusiJo added 2 commits June 17, 2025 12:55

add test paramsheet

7f89dc2

add tests

6b720d6

SusiJo force-pushed the nf-core-template-update-3.3.1 branch 2 times, most recently from 4b489d6 to 2b3f8b8 Compare June 17, 2025 13:57

update tests

7faa5f7

SusiJo force-pushed the nf-core-template-update-3.3.1 branch from 2b3f8b8 to 7faa5f7 Compare June 17, 2025 14:22

update nftignore

fa423a2

famosab reviewed Jun 18, 2025

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apply suggestions

d083b5c

famosab approved these changes Jun 18, 2025

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update snapshot

bb1a6ad

SusiJo merged commit 883ee29 into nf-core:dev Jun 23, 2025
19 checks passed

atrigila mentioned this pull request May 22, 2026

Release 2.0.0 #737

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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SusiJo commented Jun 4, 2025 •

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