Dev ratio fix channels #336

suzannejin · 2024-11-04T18:10:47Z

PR checklist

…ndance into template_up2_14_1

Template update for nf-core/tools v2.14.1

Show >10 contrasts in report

Fix pagination on samples table

Fix gprofiler2 genesets default object

Bump shinyngs, fix contrasts passed to app creation

[dev-ratio] add limma to test_experimental

add GPROFILER2 module to ENRICHMENT subworkflow

Co-authored-by: WackerO <[email protected]>

322 add module deseq2

move pathway related logic out of differential and correlation subworkflows

…for input/output channels

…od == []

github-actions · 2024-11-04T18:11:04Z

This PR is against the `master` branch ❌

Do not close this PR
Click Edit and change the base to dev
This CI test will remain failed until you push a new commit

Hi @suzannejin,

It looks like this pull-request is has been made against the suzannejin/differentialabundance master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the suzannejin/differentialabundance dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

github-actions · 2024-11-04T18:12:53Z

`nf-core pipelines lint` overall result: Failed ❌

Posted for pipeline commit 2a1d9b2

+| ✅ 317 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   5 tests had warnings |!
-| ❌   2 tests failed       |-

❌ Test failures:

nextflow_config - Config manifest.version should not contain dev for a release: 1.6.0dev
version_consistency - manifest.version was not numeric: 1.6.0dev!

❗ 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
included_configs - Pipeline config does not include custom configs. Please add the includeConfig line.

❔ 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

✅ 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 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
version_consistency - Version tags are numeric and consistent between container, release tag and config.

Run details

nf-core/tools version 3.0.2
Run at 2024-11-04 18:12:30

nf-core-bot and others added 30 commits May 8, 2024 13:58

Template update for nf-core/tools version 2.14.0

f7dabe4

Template update for nf-core/tools version 2.14.1

41729bc

Update differentialabundance_report.Rmd

d604128

Update CHANGELOG.md

20a44d6

Update CHANGELOG.md

c05522a

Merge branch 'TEMPLATE' of https://github.com/nf-core/differentialabu…

e8b0e58

…ndance into template_up2_14_1

prettier

e623b0d

Merge pull request nf-core#273 from WackerO/template_up2_14_1

cc7b3e0

Template update for nf-core/tools v2.14.1

fix files_unchanged

ab26e4c

Merge branch 'dev' into more_than_10_contrasts

62c5146

Update CHANGELOG.md

bcfde26

Merge pull request nf-core#272 from nf-core/more_than_10_contrasts

4986420

Show >10 contrasts in report

Fix pagination on samples tableee

dadf5db

Update CHANGELOG.md

04635ef

Fix CHANGELOG

8353e97

Reset versions after release

2d1f602

Fix linting

349273f

Merge pull request nf-core#274 from nf-core/fix_pagination

5ddc8dd

Fix pagination on samples table

bugfix for gprofiler without gene_sets

925527d

add comment, update changelog

ccb9aa4

simplified gene_sets logic

af2436f

Merge pull request nf-core#278 from WackerO/fix_gpro_genesets

2dce45a

Fix gprofiler2 genesets default object

bump_shinyngs

4c608da

Wire in new shinyngs log options, remove deprecated guessing option

2ab83e7

Fix contrast specification to app creation

57574cf

Can install from master now

b7af68a

Update CHANGELOG

8fb05ca

Merge pull request nf-core#280 from nf-core/bump_shinyngs

03b7984

Bump shinyngs, fix contrasts passed to app creation

add propr, mygene and fiter_var module

eff2e81

add functional subworkflows into subworkflows/local

708c4db

suzannejin and others added 27 commits October 29, 2024 12:04

fix bug

c6db7ff

change filter_difftable_limma input column names

3b398ac

add todo

f97ba6b

Merge pull request nf-core#331 from suzannejin/dev-ratio-limma

1d5b909

[dev-ratio] add limma to test_experimental

add GPROFILER2 module to ENRICHMENT subworkflow

f2b6322

Once more reorganize the pathway logic

94d3c8e

Merge remote-tracking branch 'upstream/dev-ratio' into dev-ratio

e5a5d15

add new pathway_names to test gprofiler2

02a38bb

run GPROFILER2 only when enr_method is specified in the ch_tools channel

067c592

remove trailing whitespace

47bb659

add new line at end of file

90001a2

Adapt Limma call

f7c5c77

Merge pull request nf-core#333 from nf-core/323_add_module_gprofiler2

4889998

add GPROFILER2 module to ENRICHMENT subworkflow

Merge remote-tracking branch 'upstream/dev-ratio' into dev-ratio

1198761

Implement review comments

953eb51

add deseq2 pathway name

4a5aa60

add DESEQ2 block to this workflow

3546cb0

set nsub to lower numebr given nature of test data

ba1ea24

resolve merge conflicts

d6da7ad

fix linting

a2ddd8a

update channel name to samples_and_matrix

a282a47

Co-authored-by: WackerO <[email protected]>

update channel name to samples_and_matrix

0e4a84d

Co-authored-by: WackerO <[email protected]>

update channel name to samples_and_matrix

a885116

Co-authored-by: WackerO <[email protected]>

Merge pull request nf-core#335 from nf-core/322_add_module_deseq2

0f9c9fc

322 add module deseq2

Merge pull request nf-core#318 from bjlang/dev-ratio

6d0d3b8

move pathway related logic out of differential and correlation subworkflows

fix the channels properly with the new preprocess/postprocess scheme …

1cba7e6

…for input/output channels

modify preprocess_subworkflow_input to filter the elements where meth…

2a1d9b2

…od == []

suzannejin closed this Nov 4, 2024

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Dev ratio fix channels #336

Dev ratio fix channels #336

suzannejin commented Nov 4, 2024

github-actions bot commented Nov 4, 2024

github-actions bot commented Nov 4, 2024 •

edited

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Dev ratio fix channels #336

Dev ratio fix channels #336

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suzannejin commented Nov 4, 2024

PR checklist

github-actions bot commented Nov 4, 2024

This PR is against the master branch ❌

github-actions bot commented Nov 4, 2024 • edited Loading

nf-core pipelines lint overall result: Failed ❌

❌ Test failures:

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

This PR is against the `master` branch ❌

github-actions bot commented Nov 4, 2024 •

edited

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`nf-core pipelines lint` overall result: Failed ❌