Render report when using `dream` by delfiterradas · Pull Request #607 · nf-core/differentialabundance

delfiterradas · 2026-01-12T19:57:39Z

Closes #604 and update of all modules and subworkflows.

PR checklist

github-actions · 2026-01-12T20:00:15Z

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

Posted for pipeline commit 955cecb

+| ✅ 378 tests passed       |+
#| ❔  10 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗  20 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 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

❔ 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= 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_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= 0.0
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_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_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_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_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_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_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_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: 25.04.0, Config: 25.04.0
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.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 - 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 - 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: 3.5.1
rocrate_readme_sync - RO-Crate description matches the README.md.

Run details

nf-core/tools version 3.5.1
Run at 2026-01-22 13:15:11

grst · 2026-01-13T09:00:02Z

Why does dream not have a normalized matrix? When using voom it should generate a normalized matrix just as limma does.

delfiterradas · 2026-01-13T15:18:49Z

Why does dream not have a normalized matrix? When using voom it should generate a normalized matrix just as limma does.

I am addressing this in nf-core/modules#9645.

@grst once dream generates a normalised matrix, does it still make sense that the rest of the pipeline should run even when not using voom with either limma or dream (that is, using only the raw matrix)? Or should the rest of the modules only run if a normalised matrix is created?

grst · 2026-01-13T16:03:14Z

I think it should still run, even when voom is not in use.

apeltzer

LGTM now :-)

delfiterradas added 3 commits January 12, 2026 13:55

Update limma and dream modules

3006fb2

If no normalised matrix use only raw

0a83e6f

Fix default parameters and update snapshots

09ab2d2

delfiterradas self-assigned this Jan 12, 2026

delfiterradas changed the base branch from master to dev January 12, 2026 19:57

nf-core deleted a comment from github-actions Bot Jan 12, 2026

Update CHANGELOG.md

9259845

delfiterradas and others added 8 commits January 14, 2026 15:41

Update dream and abundance_differential_filter

0cd6363

Update test params and snapshot

98f088e

Merge branch 'dev' into render_dream

d689633

Fix parameter in paramsheet

1b2f7d6

Update modules and subworkflows

7caaeed

Update snapshots

ab9a80d

Update snapshot

b4127c1

Update dream test and snapshot

e4779a5

delfiterradas marked this pull request as ready for review January 21, 2026 19:56

delfiterradas requested a review from grst January 21, 2026 20:02

grst reviewed Jan 22, 2026

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Comment thread CHANGELOG.md Outdated

Comment thread conf/paramsheet.yaml Outdated

delfiterradas and others added 5 commits January 22, 2026 09:33

Rename paramset from 'dream_rnaseq2' to 'dream_norm'

bb884c4

Rename paramset

29bbde8

Update dream test

aac6e1f

Update CHANGELOG.md

c2c61b1

Merge branch 'dev' into render_dream

955cecb

delfiterradas requested review from apeltzer and grst January 22, 2026 13:52

apeltzer approved these changes Jan 29, 2026

View reviewed changes

delfiterradas merged commit 0bf19f1 into nf-core:dev Jan 29, 2026
35 checks passed

suzannejin mentioned this pull request Jan 30, 2026

Fix parameter priority using Nextflow session variables #623

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Render report when using `dream`#607

Render report when using `dream`#607
delfiterradas merged 17 commits intonf-core:devfrom
delfiterradas:render_dream

delfiterradas commented Jan 12, 2026 •

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❗ Test warnings:

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❔ Tests fixed:

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nf-core pipelines lint overall result: Passed ✅ ⚠️

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delfiterradas commented Jan 12, 2026 •

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