Support for factors in input data

[antoniasaracco]

This closes #671

[github-actions]

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ab0bedc

+| ✅ 375 tests passed       |+
#| ❔  10 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗  19 tests had warnings |!

Details

❗ Test warnings:

• readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
• 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)
• 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

❔ 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 fixed:

• rocrate_readme_sync - Mismatch fixed: RO-Crate description updated from README.md.

✅ 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: 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 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 variable (correctly) not found: validation.failUnrecognisedParams
• nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedHeaders
• 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= abundance
• nextflow_config - Config default value correct: params.round_digits= -1
• 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_samples= 1.0
• nextflow_config - Config default value correct: params.filtering_min_proportion_not_na= 0.5
• 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_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= 0.0
• 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_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.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.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_many.nf.test' contains outdir parameter
• nf_test_content - 'tests/test_many.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/test_many.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/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_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_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_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_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_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_deseq2.nf.test' contains outdir parameter
• nf_test_content - 'tests/test_rnaseq_deseq2.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/test_rnaseq_deseq2.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/test_rnaseq_deseq2.nf.test' contains outdir parameter
• nf_test_content - 'tests/test_rnaseq_deseq2.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/test_rnaseq_deseq2.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/test_rnaseq_deseq2.nf.test' contains outdir parameter
• nf_test_content - 'tests/test_rnaseq_deseq2.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/test_rnaseq_deseq2.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/test_rnaseq_deseq2.nf.test' contains outdir parameter
• nf_test_content - 'tests/test_rnaseq_deseq2.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/test_rnaseq_deseq2.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/test_rnaseq_deseq2.nf.test' contains outdir parameter
• nf_test_content - 'tests/test_rnaseq_deseq2.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/test_rnaseq_deseq2.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: 25.10.3, Config: 25.10.3
• readme - README nf-core template version badge found.
• 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_comment.yml
• actions_schema_validation - Workflow validation passed: clean-up.yml
• actions_schema_validation - Workflow validation passed: awsfulltest.yml
• actions_schema_validation - Workflow validation passed: fix_linting.yml
• actions_schema_validation - Workflow validation passed: template-version-comment.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: download_pipeline.yml
• actions_schema_validation - Workflow validation passed: nf-test.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: release-announcements.yml
• actions_schema_validation - Workflow validation passed: awstest.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 - 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 - ABUNDANCE_DIFFERENTIAL_FILTER 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 - DREAM_NORM 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 - DIFFERENTIAL_FUNCTIONAL_ENRICHMENT 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 - 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: 3.5.1
• rocrate_readme_sync - RO-Crate description matches the README.md.

Run details

• nf-core/tools version 3.5.1
• Run at 2026-05-08 11:57:21