search

nf-core / differentialabundance

Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
https://nf-co.re/differentialabundance
MIT License
64 stars 37 forks source link

Add pipeline-level nf-tests #343

Closed atrigila closed 2 weeks ago

atrigila commented 2 weeks ago

Closes #61

PR checklist

github-actions[bot] commented 2 weeks ago

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

Posted for pipeline commit ce524ce

+| ✅ 300 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   4 tests had warnings |!
### :heavy_exclamation_mark: Test warnings: * [pipeline_todos](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/pipeline_todos) - TODO string in `main.nf`: _Optionally add in-text citation tools to this list._ * [pipeline_todos](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/pipeline_todos) - TODO string in `main.nf`: _Optionally add bibliographic entries to this list._ * [pipeline_todos](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/pipeline_todos) - TODO string in `main.nf`: _Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!_ * [pipeline_todos](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/pipeline_todos) - TODO string in `base.config`: _Check the defaults for all processes_ ### :grey_question: Tests ignored: * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File is ignored: `assets/multiqc_config.yml` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default ignored: params.report_file * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default ignored: params.logo_file * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default ignored: params.css_file * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default ignored: params.citations_file * [multiqc_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/multiqc_config) - multiqc_config ### :white_check_mark: Tests passed: * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `.gitattributes` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `.gitignore` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `.nf-core.yml` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `.editorconfig` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `.prettierignore` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `.prettierrc.yml` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `CHANGELOG.md` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `CITATIONS.md` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `CODE_OF_CONDUCT.md` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `LICENSE` or `LICENSE.md` or `LICENCE` or `LICENCE.md` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `nextflow_schema.json` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `nextflow.config` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `README.md` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `.github/.dockstore.yml` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `.github/CONTRIBUTING.md` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `.github/ISSUE_TEMPLATE/bug_report.yml` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `.github/ISSUE_TEMPLATE/config.yml` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `.github/ISSUE_TEMPLATE/feature_request.yml` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `.github/PULL_REQUEST_TEMPLATE.md` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `.github/workflows/branch.yml` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `.github/workflows/ci.yml` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `.github/workflows/linting_comment.yml` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `.github/workflows/linting.yml` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `assets/email_template.html` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `assets/email_template.txt` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `assets/sendmail_template.txt` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `assets/nf-core-differentialabundance_logo_light.png` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `conf/modules.config` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `conf/test.config` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `conf/test_full.config` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `docs/images/nf-core-differentialabundance_logo_light.png` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `docs/images/nf-core-differentialabundance_logo_dark.png` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `docs/output.md` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `docs/README.md` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `docs/README.md` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `docs/usage.md` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `main.nf` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `conf/base.config` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `conf/igenomes.config` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `conf/igenomes_ignored.config` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `.github/workflows/awstest.yml` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `.github/workflows/awsfulltest.yml` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `modules.json` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `.github/ISSUE_TEMPLATE/bug_report.md` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `.github/ISSUE_TEMPLATE/feature_request.md` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `.github/workflows/push_dockerhub.yml` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `.markdownlint.yml` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `.nf-core.yaml` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `.yamllint.yml` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `bin/markdown_to_html.r` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `conf/aws.config` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `docs/images/nf-core-differentialabundance_logo.png` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `lib/Checks.groovy` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `lib/Completion.groovy` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `lib/NfcoreTemplate.groovy` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `lib/Utils.groovy` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `lib/Workflow.groovy` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `lib/WorkflowMain.groovy` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `lib/WorkflowDifferentialabundance.groovy` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `parameters.settings.json` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `pipeline_template.yml` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `Singularity` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `lib/nfcore_external_java_deps.jar` * [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `.travis.yml` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Found nf-schema plugin * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.name` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.nextflowVersion` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.description` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.version` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.homePage` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `timeline.enabled` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `trace.enabled` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `report.enabled` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `dag.enabled` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `process.cpus` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `process.memory` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `process.time` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `params.outdir` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `params.input` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `validation.help.enabled` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.mainScript` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `timeline.file` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `trace.file` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `report.file` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `dag.file` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `validation.help.beforeText` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `validation.help.afterText` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `validation.help.command` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `validation.summary.beforeText` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `validation.summary.afterText` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.nf_required_version` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.container` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.singleEnd` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.igenomesIgnore` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.name` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.enable_conda` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.max_cpus` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.max_memory` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.max_time` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.validationFailUnrecognisedParams` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.validationLenientMode` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.validationSchemaIgnoreParams` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.validationShowHiddenParams` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config ``timeline.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config ``report.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config ``trace.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config ``dag.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config ``manifest.name`` began with ``nf-core/`` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable ``manifest.homePage`` began with https://github.com/nf-core/ * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config ``dag.file`` ended with ``.html`` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable ``manifest.nextflowVersion`` started with >= or !>= * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config ``manifest.version`` ends in ``dev``: ``1.6.0dev`` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config `params.custom_config_version` is set to `master` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config `params.custom_config_base` is set to `https://raw.githubusercontent.com/nf-core/configs/master` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Lines for loading custom profiles found * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - nextflow.config contains configuration profile `test` * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.study_name= study * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.study_type= rnaseq * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.study_abundance_type= counts * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.affy_cel_files_archive= null * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.querygse= null * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.observations_id_col= sample * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.observations_type= sample * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.features_id_col= gene_id * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.features_name_col= gene_name * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.features_type= gene * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.features_metadata_cols= gene_id,gene_name,gene_biotype * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.features_gtf_feature_type= transcript * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.features_gtf_table_first_field= gene_id * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.affy_file_name_col= file * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.affy_background= true * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.affy_bgversion= 2 * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.affy_cdfname= null * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.affy_build_annotation= true * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.proteus_measurecol_prefix= LFQ intensity * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.proteus_norm_function= normalizeMedian * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.proteus_plotsd_method= violin * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.proteus_plotmv_loess= true * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.proteus_palette_name= Set1 * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.filtering_min_abundance= 1.0 * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.filtering_min_samples= 1.0 * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.filtering_min_proportion_not_na= 0.5 * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.exploratory_clustering_method= ward.D2 * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.exploratory_cor_method= spearman * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.exploratory_n_features= 500 * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.exploratory_whisker_distance= 1.5 * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.exploratory_mad_threshold= -5 * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.exploratory_main_variable= auto_pca * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.exploratory_assay_names= raw,normalised,variance_stabilised * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.exploratory_final_assay= variance_stabilised * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.exploratory_palette_name= Set1 * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.differential_feature_id_column= gene_id * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.differential_fc_column= log2FoldChange * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.differential_pval_column= pvalue * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.differential_qval_column= padj * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.differential_min_fold_change= 2.0 * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.differential_max_pval= 1.0 * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.differential_max_qval= 0.05 * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.differential_feature_name_column= gene_name * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.differential_foldchanges_logged= true * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.differential_palette_name= Set1 * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.deseq2_test= Wald * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.deseq2_fit_type= parametric * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.deseq2_sf_type= ratio * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.deseq2_min_replicates_for_replace= 7 * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.deseq2_independent_filtering= true * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.deseq2_lfc_threshold= 0 * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.deseq2_alt_hypothesis= greaterAbs * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.deseq2_p_adjust_method= BH * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.deseq2_alpha= 0.1 * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.deseq2_minmu= 0.5 * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.deseq2_vs_method= vst * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.deseq2_shrink_lfc= true * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.deseq2_cores= 1 * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.deseq2_vs_blind= true * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.deseq2_vst_nsub= 1000 * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.limma_spacing= null * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.limma_block= null * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.limma_correlation= null * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.limma_method= ls * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.limma_proportion= 0.01 * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.limma_stdev_coef_lim= 0.1,4 * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.limma_winsor_tail_p= 0.05,0.1 * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.limma_lfc= 0 * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.limma_adjust_method= BH * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.limma_p_value= 1.0 * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.limma_use_voom= false * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.gsea_permute= phenotype * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.gsea_nperm= 1000 * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.gsea_scoring_scheme= weighted * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.gsea_metric= Signal2Noise * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.gsea_sort= real * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.gsea_order= descending * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.gsea_set_max= 500 * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.gsea_set_min= 15 * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.gsea_norm= meandiv * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.gsea_rnd_type= no_balance * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.gsea_make_sets= true * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.gsea_num= 100 * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.gsea_plot_top_x= 20 * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.gsea_rnd_seed= timestamp * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.gprofiler2_significant= true * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.gprofiler2_measure_underrepresentation= false * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.gprofiler2_evcodes= false * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.gprofiler2_max_qval= 0.05 * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.gprofiler2_domain_scope= annotated * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.gprofiler2_min_diff= 1 * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.gprofiler2_palette_name= Blues * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.shinyngs_build_app= true * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.shinyngs_shinyapps_account= null * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.shinyngs_shinyapps_app_name= null * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.gene_sets_files= null * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.report_title= null * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.report_author= null * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.report_description= null * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.report_scree= true * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.report_round_digits= 4 * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/ * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.custom_config_version= master * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.publish_dir_mode= copy * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.validate_params= true * [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/ * [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `.gitattributes` matches the template * [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `.prettierrc.yml` matches the template * [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `CODE_OF_CONDUCT.md` matches the template * [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `LICENSE` matches the template * [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `.github/.dockstore.yml` matches the template * [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `.github/CONTRIBUTING.md` matches the template * [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `.github/ISSUE_TEMPLATE/bug_report.yml` matches the template * [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `.github/ISSUE_TEMPLATE/config.yml` matches the template * [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `.github/ISSUE_TEMPLATE/feature_request.yml` matches the template * [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `.github/PULL_REQUEST_TEMPLATE.md` matches the template * [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `.github/workflows/branch.yml` matches the template * [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `.github/workflows/linting_comment.yml` matches the template * [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `.github/workflows/linting.yml` matches the template * [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `assets/email_template.html` matches the template * [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `assets/email_template.txt` matches the template * [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `assets/sendmail_template.txt` matches the template * [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `assets/nf-core-differentialabundance_logo_light.png` matches the template * [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `docs/images/nf-core-differentialabundance_logo_light.png` matches the template * [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `docs/images/nf-core-differentialabundance_logo_dark.png` matches the template * [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `docs/README.md` matches the template * [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `.gitignore` matches the template * [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `.prettierignore` matches the template * [actions_ci](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/actions_ci) - '.github/workflows/ci.yml' is triggered on expected events * [actions_ci](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/actions_ci) - '.github/workflows/ci.yml' checks minimum NF version * [actions_awstest](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/actions_awstest) - '.github/workflows/awstest.yml' is triggered correctly * [actions_awsfulltest](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/actions_awsfulltest) - `.github/workflows/awsfulltest.yml` is triggered correctly * [actions_awsfulltest](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/actions_awsfulltest) - `.github/workflows/awsfulltest.yml` does not use `-profile test` * [readme](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/readme) - README Nextflow minimum version badge matched config. Badge: `24.04.2`, Config: `24.04.2` * [readme](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/readme) - README Zenodo placeholder was replaced with DOI. * [plugin_includes](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/plugin_includes) - No wrong validation plugin imports have been found * [pipeline_name_conventions](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/pipeline_name_conventions) - Name adheres to nf-core convention * [template_strings](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/template_strings) - Did not find any Jinja template strings (0 files) * [schema_lint](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/schema_lint) - Schema lint passed * [schema_lint](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/schema_lint) - Schema title + description lint passed * [schema_lint](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/schema_lint) - Input mimetype lint passed: 'text/csv' * [schema_params](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/schema_params) - Schema matched params returned from nextflow config * [system_exit](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/system_exit) - No `System.exit` calls found * [actions_schema_validation](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: linting.yml * [actions_schema_validation](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: branch.yml * [actions_schema_validation](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: fix-linting.yml * [actions_schema_validation](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: release-announcements.yml * [actions_schema_validation](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: awsfulltest.yml * [actions_schema_validation](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: template_version_comment.yml * [actions_schema_validation](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: download_pipeline.yml * [actions_schema_validation](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: ci.yml * [actions_schema_validation](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: clean-up.yml * [actions_schema_validation](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: awstest.yml * [actions_schema_validation](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: linting_comment.yml * [merge_markers](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/merge_markers) - No merge markers found in pipeline files * [modules_json](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_json) - Only installed modules found in `modules.json` * [modules_structure](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_structure) - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL' * [base_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/base_config) - `conf/base.config` found and not ignored. * [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `conf/modules.config` found and not ignored. * [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `GUNZIP_GTF` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `GTF_TO_TABLE` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `VALIDATOR` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `AFFY_JUSTRMA_RAW` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `AFFY_JUSTRMA_NORM` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `PROTEUS` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `GEOQUERY_GETGEO` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `DESEQ2_NORM` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `DESEQ2_DIFFERENTIAL` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `LIMMA_DIFFERENTIAL` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `FILTER_DIFFTABLE` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `GSEA_GSEA` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `GPROFILER2_GOST` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `PLOT_EXPLORATORY` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `PLOT_DIFFERENTIAL` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `SHINYNGS_APP` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `RMARKDOWNNOTEBOOK` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `MAKE_REPORT_BUNDLE` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `CUSTOM_MATRIXFILTER` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `CUSTOM_TABULARTOGSEACLS` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `CUSTOM_TABULARTOGSEAGCT` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `TABULAR_TO_GSEA_CHIP` found in `conf/modules.config` and Nextflow scripts. * [nfcore_yml](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nfcore_yml) - Repository type in `.nf-core.yml` is valid: `pipeline` * [nfcore_yml](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nfcore_yml) - nf-core version in `.nf-core.yml` is set to the latest version: `3.0.2` ### Run details * nf-core/tools version 3.0.2 * Run at `2024-11-11 14:11:45`
pinin4fjords commented 2 weeks ago

Looks great, love the new nf-test implementation, so much simple. Regarding @pinin4fjords comment about sharding, I also think it is easier to understand the tests, but I'm curious to know if we use sharding to make tests run faster or to save costs. If it is the latter, isn't it better to have it, even if reading the tests is a little bit harder?

As I understand it the sharding was introduced to bypass GitHub's limits on the numbers of independent tests, not out of any consideration to costs. In any case, my time is more valuable than computer time, so I'd like to save myself squinting at inscrutable test names.

atrigila commented 2 weeks ago

@pinin4fjords done :) thank you!