Dev ratio

Open bjlang opened this issue 1 year ago • 1 comments

PR checklist

[ ] This comment contains a description of changes (with reason).
[ ] If you've fixed a bug or added code that should be tested, add tests!
[ ] If you've added a new tool - have you followed the pipeline conventions in the contribution docs
[ ] If necessary, also make a PR on the nf-core/differentialabundance branch on the nf-core/test-datasets repository.
[x] Make sure your code lints (nf-core lint).
[x] Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
[ ] Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
[ ] Usage Documentation in docs/usage.md is updated.
[ ] Output Documentation in docs/output.md is updated.
[ ] CHANGELOG.md is updated.
[ ] README.md is updated (including new tool citations and authors/contributors).

Sep 13 '24 13:09 bjlang

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

Posted for pipeline commit 0329206

+| ✅ 317 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   4 tests had warnings |!

:heavy_exclamation_mark: Test warnings:

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

:grey_question: Tests ignored:

files_exist - File is ignored: assets/multiqc_config.yml
nextflow_config - Config default ignored: params.tools
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
multiqc_config - multiqc_config

:white_check_mark: Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .editorconfig
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/ci.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: 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 not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: docs/images/nf-core-differentialabundance_logo.png
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowDifferentialabundance.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nextflow_config - Found nf-schema plugin
nextflow_config - Config variable found: manifest.name
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: manifest.homePage
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: validation.help.enabled
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable found: validation.help.beforeText
nextflow_config - Config variable found: validation.help.afterText
nextflow_config - Config variable found: validation.help.command
nextflow_config - Config variable found: validation.summary.beforeText
nextflow_config - Config variable found: validation.summary.afterText
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config variable (correctly) not found: params.max_cpus
nextflow_config - Config variable (correctly) not found: params.max_memory
nextflow_config - Config variable (correctly) not found: params.max_time
nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
nextflow_config - Config variable (correctly) not found: params.validationLenientMode
nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version ends in dev: 1.6.0dev
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.study_name= study
nextflow_config - Config default value correct: params.study_type= rnaseq
nextflow_config - Config default value correct: params.study_abundance_type= counts
nextflow_config - Config default value correct: params.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.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.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_cdfname= null
nextflow_config - Config default value correct: params.affy_build_annotation= true
nextflow_config - Config default value correct: params.proteus_measurecol_prefix= LFQ intensity
nextflow_config - Config default value correct: params.proteus_norm_function= normalizeMedian
nextflow_config - Config default value correct: params.proteus_plotsd_method= violin
nextflow_config - Config default value correct: params.proteus_plotmv_loess= true
nextflow_config - Config default value correct: params.proteus_palette_name= Set1
nextflow_config - Config default value correct: params.filtering_min_abundance= 1.0
nextflow_config - Config default value correct: params.filtering_min_samples= 1.0
nextflow_config - Config default value correct: params.filtering_min_proportion_not_na= 0.5
nextflow_config - Config default value correct: params.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_palette_name= Set1
nextflow_config - Config default value correct: params.differential_feature_id_column= gene_id
nextflow_config - Config default value correct: params.differential_fc_column= log2FoldChange
nextflow_config - Config default value correct: params.differential_pval_column= pvalue
nextflow_config - Config default value correct: params.differential_qval_column= padj
nextflow_config - Config default value correct: params.differential_min_fold_change= 2.0
nextflow_config - Config default value correct: params.differential_max_pval= 1.0
nextflow_config - Config default value correct: params.differential_max_qval= 0.05
nextflow_config - Config default value correct: params.differential_feature_name_column= gene_name
nextflow_config - Config default value correct: params.differential_foldchanges_logged= true
nextflow_config - Config default value correct: params.differential_palette_name= Set1
nextflow_config - Config default value correct: params.deseq2_test= Wald
nextflow_config - Config default value correct: params.deseq2_fit_type= parametric
nextflow_config - Config default value correct: params.deseq2_sf_type= ratio
nextflow_config - Config default value correct: params.deseq2_min_replicates_for_replace= 7
nextflow_config - Config default value correct: params.deseq2_independent_filtering= true
nextflow_config - Config default value correct: params.deseq2_lfc_threshold= 0
nextflow_config - Config default value correct: params.deseq2_alt_hypothesis= greaterAbs
nextflow_config - Config default value correct: params.deseq2_p_adjust_method= BH
nextflow_config - Config default value correct: params.deseq2_alpha= 0.1
nextflow_config - Config default value correct: params.deseq2_minmu= 0.5
nextflow_config - Config default value correct: params.deseq2_vs_method= vst
nextflow_config - Config default value correct: params.deseq2_shrink_lfc= true
nextflow_config - Config default value correct: params.deseq2_cores= 1
nextflow_config - Config default value correct: params.deseq2_vs_blind= true
nextflow_config - Config default value correct: params.deseq2_vst_nsub= 1000
nextflow_config - Config default value correct: params.limma_spacing= null
nextflow_config - Config default value correct: params.limma_block= null
nextflow_config - Config default value correct: params.limma_correlation= null
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.propd_alpha= null
nextflow_config - Config default value correct: params.propd_moderated= true
nextflow_config - Config default value correct: params.propd_fdr= 0.05
nextflow_config - Config default value correct: params.propd_permutation= 0
nextflow_config - Config default value correct: params.propd_ncutoffs= 100
nextflow_config - Config default value correct: params.propd_weighted_degree= false
nextflow_config - Config default value correct: params.propr_metric= rho
nextflow_config - Config default value correct: params.propr_ivar= clr
nextflow_config - Config default value correct: params.propr_alpha= null
nextflow_config - Config default value correct: params.propr_fdr= 0.05
nextflow_config - Config default value correct: params.propr_permutation= 100
nextflow_config - Config default value correct: params.propr_ncutoffs= 100
nextflow_config - Config default value correct: params.propr_tails= right
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_measure_underrepresentation= false
nextflow_config - Config default value correct: params.gprofiler2_evcodes= false
nextflow_config - Config default value correct: params.gprofiler2_max_qval= 0.05
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.grea_set_min= 15
nextflow_config - Config default value correct: params.grea_set_max= 500
nextflow_config - Config default value correct: params.grea_permutation= 100
nextflow_config - Config default value correct: params.shinyngs_build_app= true
nextflow_config - Config default value correct: params.shinyngs_shinyapps_account= null
nextflow_config - Config default value correct: params.shinyngs_shinyapps_app_name= null
nextflow_config - Config default value correct: params.gene_sets_files= null
nextflow_config - Config default value correct: params.report_title= null
nextflow_config - Config default value correct: params.report_author= null
nextflow_config - Config default value correct: params.report_description= null
nextflow_config - Config default value correct: params.report_scree= true
nextflow_config - Config default value correct: params.report_round_digits= 4
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/
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/CONTRIBUTING.md 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 - assets/nf-core-differentialabundance_logo_light.png matches the template
files_unchanged - docs/images/nf-core-differentialabundance_logo_light.png matches the template
files_unchanged - docs/images/nf-core-differentialabundance_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.yml' checks minimum NF version
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 24.04.2, Config: 24.04.2
readme - README Zenodo placeholder was replaced with DOI.
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_lint - Input mimetype lint passed: 'text/csv'
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: branch.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: template_version_comment.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
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 - 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_DIFFERENTIAL found in conf/modules.config and Nextflow scripts.
modules_config - FILTER_DIFFTABLE found in conf/modules.config and Nextflow scripts.
modules_config - GSEA_GSEA found in conf/modules.config and Nextflow scripts.
modules_config - GPROFILER2_GOST found in conf/modules.config and Nextflow scripts.
modules_config - PLOT_EXPLORATORY found in conf/modules.config and Nextflow scripts.
modules_config - PLOT_DIFFERENTIAL found in conf/modules.config and Nextflow scripts.
modules_config - SHINYNGS_APP found in conf/modules.config and Nextflow scripts.
modules_config - RMARKDOWNNOTEBOOK found in conf/modules.config and Nextflow scripts.
modules_config - MAKE_REPORT_BUNDLE found in conf/modules.config and Nextflow scripts.
modules_config - CUSTOM_MATRIXFILTER 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 - TABULAR_TO_GSEA_CHIP found in conf/modules.config and Nextflow scripts.
modules_config - PROPR found in conf/modules.config and Nextflow scripts.
modules_config - PROPD found in conf/modules.config and Nextflow scripts.
modules_config - GREA found in conf/modules.config and Nextflow scripts.
modules_config - MYGENE 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: 3.0.2

Run details

nf-core/tools version 3.0.2
Run at 2024-10-28 11:24:12

Sep 13 '24 13:09 github-actions[bot]

[x] just finished adding the updated local modules propr/propr propr/propd and propr/grea

Oct 10 '24 09:10 suzannejin

[x] added default parameters for propd/propr/grea modules. Still need to find a better way to handle them though, see discussion in #302

Oct 22 '24 08:10 suzannejin

close pr as it is treated in #431 and #385

Feb 14 '25 10:02 suzannejin

Dev ratio

PR checklist

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

:heavy_exclamation_mark: Test warnings:

:grey_question: Tests ignored:

:white_check_mark: Tests passed:

Run details

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