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Merge branch 'dev' into decoupler_2
2 parents ff2655f + ecfdc89 commit 558f9e6

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+129
-84
lines changed

‎CHANGELOG.md‎

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@@ -25,6 +25,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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### Fixed
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- [[#476](https://github.com/nf-core/differentialabundance/pull/476)] - Fixed null.csv and warning at top of report ([@SusiJo](https://github.com/SusiJo), reviewed by [@pinin4fjords](https://github.com/pinin4fjords), [@atrigila](https://github.com/atrigila), [@maxulysse](https://github.com/maxulysse))
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- [[#358](https://github.com/nf-core/differentialabundance/pull/358)] - Fixed nf-tests not running due to `--changed-since HEAD^`([@atrigila](https://github.com/atrigila), review by [@pinin4fjords](https://github.com/pinin4fjords))
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- [[#344](https://github.com/nf-core/differentialabundance/pull/344)] - Fixed replacement of NA sub-strings
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([@atrigila](https://github.com/atrigila), suggested by [@BEFH](https://github.com/BEFH), review by [@apeltzer](https://github.com/apeltzer) and [@nschcolnicov](https://github.com/nschcolnicov))
@@ -40,6 +41,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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### Changed
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- [[#476](https://github.com/nf-core/differentialabundance/pull/476)] - Update documentation & report fixes ([@SusiJo](https://github.com/SusiJo), reviewed by [@pinin4fjords](https://github.com/pinin4fjords), [@atrigila](https://github.com/atrigila), [@maxulysse](https://github.com/maxulysse))
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- [[#468](https://github.com/nf-core/differentialabundance/pull/468)] - Template update for nf-core/tools v3.3.1 ([@SusiJo](https://github.com/SusiJo), reviewed by [@famosab](https://github.com/famosab), [@mashehu](https://github.com/mashehu))
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- [[#448](https://github.com/nf-core/differentialabundance/pull/448)] - Simplify toolsheet handling and restructure workflow to use paramset in meta. ([@pinin4fjords](https://github.com/pinin4fjords), review by [@suzannejin](https://github.com/suzannejin) and [@grst](https://github.com/grst))
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- [[#431](https://github.com/nf-core/differentialabundance/pull/431)] - Replace the calls to differential and functional analysis modules by subworkflows. ([@suzannejin](https://github.com/suzannejin), review by [@pinin4fjords](https://github.com/pinin4fjords))

‎assets/differentialabundance_report.Rmd‎

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@@ -220,7 +220,7 @@ report_subtitle <- paste0(ifelse(is.null(params$report_author), '', paste0('By '
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```
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---
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title: "<img src=\"`r file.path(params$input_dir, params$logo)`\" style=\"float: left;\"/>`r report_title`"
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title: "<img id=\"logo\" src=\"`r file.path(params$input_dir, params$logo)`\" style=\"float: left;\"/>`r report_title`"
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subtitle: `r report_subtitle`
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---
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\
@@ -987,8 +987,8 @@ if (!is.null(params$functional_method)){
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gmt_name <- basename(tools::file_path_sans_ext(gmt_file))
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cat("\n##### ", gmt_name ," {.tabset}\n")
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reference_gsea_tables <- paste0(differential_names, ".", gmt_name, '.gsea_report_for_', gsea_contrasts$reference, '.tsv')
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target_gsea_tables <- paste0(differential_names, ".", gmt_name, '.gsea_report_for_', gsea_contrasts$target, '.tsv')
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reference_gsea_tables <- paste0(gsea_contrasts$id, ".", gmt_name, '.gsea_report_for_', gsea_contrasts$reference, '.tsv')
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target_gsea_tables <- paste0(gsea_contrasts$id, ".", gmt_name, '.gsea_report_for_', gsea_contrasts$target, '.tsv')
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for (i in seq_len(nrow(gsea_contrasts))) {
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cat("\n###### ", contrast_descriptions[i], "\n")
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ifelse(params$gprofiler2_significant, paste0(" Enrichment was only considered if significant, i.e. adjusted p-value <= ", params$gprofiler2_max_qval, "."), "Enrichment was also considered if not significant."), "\n"))
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# Make sure to grab only non-empty files
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for (name in differential_names) {
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for (i in seq_along(differential_names)) {
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name <- differential_names[i]
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cat(paste0("\n##### ", name, "\n"))
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table <- paste0(name, ".gprofiler2.all_enriched_pathways.tsv")
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table <- paste0(contrasts$id[i], ".gprofiler2.all_enriched_pathways.tsv")
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table_path <- file.path(params$input_dir, table)
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if (!file.exists(table_path) || file.size(table_path) == 0){
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cat(paste0("No ", ifelse(params$gprofiler2_significant, "significantly", ""), " enriched pathways were found for this contrast."))

‎nextflow_schema.json‎

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‎subworkflows/local/utils_nfcore_differentialabundance_pipeline/main.nf‎

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@@ -373,8 +373,8 @@ def getParamsheetConfigurations() {
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// Get default configurations from pipeline parameters
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def getDefaultConfigurations() {
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// replace null by string 'null' for paramset_name to avoid certain problems with null object
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return [params + [paramset_name: 'null']]
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// replace null by string 'contrasts' for paramset_name to avoid certain problems with null object
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return [params + [paramset_name: 'contrasts']]
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}
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// Create a temporary schema file for paramsheet validation

‎tests/.nftignore‎

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pipeline_info/*.{html,json,txt,yml}
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report/gsea/**/*.symbols.Gsea.rpt
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report/gsea/**/*.{rpt,html,png}
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**/**/*.{gprofiler2.*.rds,gprofiler2.*.html}
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report/*.html
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report/*.zip
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report/*.png

‎tests/default.nf.test‎

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@@ -104,6 +104,7 @@ nextflow_pipeline {
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outdir = "$outputDir"
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differential_method = 'deseq2'
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functional_method = 'gprofiler2'
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gprofiler2_organism = 'mmusculus'
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input = 'https://github.com/nf-core/test-datasets/raw/differentialabundance/modules_testdata/variancepartition_dream/metadata.tsv'
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matrix = 'https://github.com/nf-core/test-datasets/raw/differentialabundance/modules_testdata/variancepartition_dream/counts.tsv'
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contrasts_yml = 'https://github.com/nf-core/test-datasets/raw/differentialabundance/testdata/formula_contrasts/rnaseq_complex_contrast.yaml'

‎tests/default.nf.test.snap‎

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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "25.04.3"
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"nextflow": "25.04.6"
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},
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"timestamp": "2025-06-23T09:03:01.551039804"
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"timestamp": "2025-09-19T08:59:25.110233661"
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},
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"Test profile - with toolsheet": {
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"content": [
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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "25.04.3"
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"nextflow": "25.04.6"
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},
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"timestamp": "2025-06-23T09:01:41.694097903"
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"timestamp": "2025-09-19T08:58:04.654957304"
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},
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"Test profile - with toolsheet and formula": {
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"content": [
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"other/gprofiler2/full_model_with_interactions_SRP254919",
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"other/gprofiler2/interaction_genotype_treatment_SRP254919",
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"other/gprofiler2/treatment_effect_classic_comparison_SRP254919",
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"other/gprofiler2/treatment_effect_classic_comparison_SRP254919.gprofiler2.gost_results.rds",
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"other/gprofiler2/treatment_effect_classic_comparison_SRP254919/treatment_effect_classic_comparison_SRP254919.gprofiler2.gost_results.rds",
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"other/gprofiler2/treatment_plus_genotype_SRP254919",
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"other/gprofiler2/treatment_plus_genotype_SRP254919.gprofiler2.gost_results.rds",
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"other/gprofiler2/treatment_plus_genotype_SRP254919/treatment_plus_genotype_SRP254919.gprofiler2.gost_results.rds",
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"pipeline_info",
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"pipeline_info/collated_versions.yml",
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"pipeline_info/nf_core_differentialabundance_software_versions.yml",
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"plots/gprofiler2/full_model_with_interactions_SRP254919",
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"plots/gprofiler2/interaction_genotype_treatment_SRP254919",
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"plots/gprofiler2/treatment_effect_classic_comparison_SRP254919",
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"plots/gprofiler2/treatment_effect_classic_comparison_SRP254919/treatment_effect_classic_comparison_SRP254919.gprofiler2.CORUM.sub_enriched_pathways.png",
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"plots/gprofiler2/treatment_effect_classic_comparison_SRP254919/treatment_effect_classic_comparison_SRP254919.gprofiler2.HP.sub_enriched_pathways.png",
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"plots/gprofiler2/treatment_effect_classic_comparison_SRP254919/treatment_effect_classic_comparison_SRP254919.gprofiler2.KEGG.sub_enriched_pathways.png",
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"plots/gprofiler2/treatment_effect_classic_comparison_SRP254919/treatment_effect_classic_comparison_SRP254919.gprofiler2.REAC.sub_enriched_pathways.png",
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"plots/gprofiler2/treatment_effect_classic_comparison_SRP254919/treatment_effect_classic_comparison_SRP254919.gprofiler2.gostplot.html",
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"plots/gprofiler2/treatment_effect_classic_comparison_SRP254919/treatment_effect_classic_comparison_SRP254919.gprofiler2.gostplot.png",
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"plots/gprofiler2/treatment_plus_genotype_SRP254919",
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"plots/gprofiler2/treatment_plus_genotype_SRP254919/treatment_plus_genotype_SRP254919.gprofiler2.HP.sub_enriched_pathways.png",
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"plots/gprofiler2/treatment_plus_genotype_SRP254919/treatment_plus_genotype_SRP254919.gprofiler2.TF.sub_enriched_pathways.png",
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"plots/gprofiler2/treatment_plus_genotype_SRP254919/treatment_plus_genotype_SRP254919.gprofiler2.gostplot.html",
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"plots/gprofiler2/treatment_plus_genotype_SRP254919/treatment_plus_genotype_SRP254919.gprofiler2.gostplot.png",
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"plots/qc",
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"plots/qc/full_model_with_interactions_SRP254919.deseq2.dispersion.png",
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"plots/qc/interaction_genotype_treatment_SRP254919.deseq2.dispersion.png",
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"tables/gprofiler2/interaction_genotype_treatment_SRP254919",
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"tables/gprofiler2/interaction_genotype_treatment_SRP254919/interaction_genotype_treatment_SRP254919.gprofiler2.all_enriched_pathways.tsv",
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"tables/gprofiler2/treatment_effect_classic_comparison_SRP254919",
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"tables/gprofiler2/treatment_effect_classic_comparison_SRP254919/treatment_effect_classic_comparison_SRP254919.gprofiler2.CORUM.sub_enriched_pathways.tsv",
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"tables/gprofiler2/treatment_effect_classic_comparison_SRP254919/treatment_effect_classic_comparison_SRP254919.gprofiler2.HP.sub_enriched_pathways.tsv",
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"tables/gprofiler2/treatment_effect_classic_comparison_SRP254919/treatment_effect_classic_comparison_SRP254919.gprofiler2.KEGG.sub_enriched_pathways.tsv",
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"tables/gprofiler2/treatment_effect_classic_comparison_SRP254919/treatment_effect_classic_comparison_SRP254919.gprofiler2.REAC.sub_enriched_pathways.tsv",
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"tables/gprofiler2/treatment_effect_classic_comparison_SRP254919/treatment_effect_classic_comparison_SRP254919.gprofiler2.all_enriched_pathways.tsv",
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"tables/gprofiler2/treatment_plus_genotype_SRP254919",
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"tables/gprofiler2/treatment_plus_genotype_SRP254919/treatment_plus_genotype_SRP254919.gprofiler2.HP.sub_enriched_pathways.tsv",
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"tables/gprofiler2/treatment_plus_genotype_SRP254919/treatment_plus_genotype_SRP254919.gprofiler2.TF.sub_enriched_pathways.tsv",
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"tables/gprofiler2/treatment_plus_genotype_SRP254919/treatment_plus_genotype_SRP254919.gprofiler2.all_enriched_pathways.tsv",
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"tables/processed_abundance",
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"tables/processed_abundance/all.normalised_counts.tsv",
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"treatment_effect_classic_comparison_SRP254919.deseq2.results_filtered.tsv:md5,65e7a9d354eb71db7f13576cc2d5d7e7",
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"full_model_with_interactions_SRP254919.gprofiler2.all_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
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"interaction_genotype_treatment_SRP254919.gprofiler2.all_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
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"treatment_effect_classic_comparison_SRP254919.gprofiler2.all_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
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"treatment_plus_genotype_SRP254919.gprofiler2.all_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
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"treatment_effect_classic_comparison_SRP254919.gprofiler2.CORUM.sub_enriched_pathways.tsv:md5,d7dca3803318350b7d3328dc14e8846b",
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"treatment_effect_classic_comparison_SRP254919.gprofiler2.HP.sub_enriched_pathways.tsv:md5,6c2249f6a9b4eb5ee0168fa44a670dea",
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"treatment_effect_classic_comparison_SRP254919.gprofiler2.KEGG.sub_enriched_pathways.tsv:md5,58c77b638e8b4e02cd486cf6b03d5ab6",
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"treatment_effect_classic_comparison_SRP254919.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,0790f8beea2055f927741b27eb675e7b",
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"treatment_effect_classic_comparison_SRP254919.gprofiler2.all_enriched_pathways.tsv:md5,7988d05d69d9f17b654d4a8a514fa5c7",
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"treatment_plus_genotype_SRP254919.gprofiler2.HP.sub_enriched_pathways.tsv:md5,1e67df6e7e51f8d733714e25d61db06d",
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"treatment_plus_genotype_SRP254919.gprofiler2.TF.sub_enriched_pathways.tsv:md5,704e772ab4c6b8e6768d7dd8abb370bd",
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"treatment_plus_genotype_SRP254919.gprofiler2.all_enriched_pathways.tsv:md5,9cf6caebcf0b59460cefc5d3532207ee",
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"all.normalised_counts.tsv:md5,c2d7cc11637ad01ea49fff4a744965c9",
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"all.rlog.tsv:md5,bce2521996537372c72f4083f66c5d3b"
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]
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"nf-test": "0.9.2",
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"nextflow": "25.04.6"
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},
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"timestamp": "2025-07-24T16:46:01.377784674"
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"timestamp": "2025-09-04T13:41:25.55678279"
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},
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"Test profile - yml no formula": {
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"content": [
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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "25.04.3"
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"nextflow": "25.04.6"
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},
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"timestamp": "2025-06-23T09:04:21.203865649"
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"timestamp": "2025-09-19T09:00:45.008596168"
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}
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}

‎tests/test_affy.nf.test.snap‎

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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "25.04.3"
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"nextflow": "25.04.6"
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},
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"timestamp": "2025-06-17T15:17:08.723393528"
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"timestamp": "2025-09-19T09:05:43.521907455"
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},
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"Test affy profile - with toolsheet": {
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"content": [
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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "25.04.3"
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"nextflow": "25.04.6"
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},
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"timestamp": "2025-06-17T15:20:21.3699015"
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"timestamp": "2025-09-19T09:08:57.977766595"
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}
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}

‎tests/test_custom_paramsheet.nf.test‎

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outdir = "$outputDir"
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paramsheet = "https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/differentialabundance/testdata/test_custom_paramsheet.csv"
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paramset_name = "gprofiler2"
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gprofiler2_organism = 'mmusculus'
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// input data
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input = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.csv'

‎tests/test_custom_paramsheet.nf.test.snap‎

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"other/gprofiler2",
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"other/gprofiler2/treatment_mCherry_hND6__SRP254919",
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"other/gprofiler2/treatment_mCherry_hND6_sample_number_SRP254919",
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"other/gprofiler2/treatment_mCherry_hND6_sample_number_SRP254919.gprofiler2.gost_results.rds",
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"other/gprofiler2/treatment_mCherry_hND6_sample_number_SRP254919/treatment_mCherry_hND6_sample_number_SRP254919.gprofiler2.gost_results.rds",
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"pipeline_info",
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"pipeline_info/collated_versions.yml",
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"plots/gprofiler2/treatment_mCherry_hND6_sample_number_SRP254919",
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"plots/gprofiler2/treatment_mCherry_hND6_sample_number_SRP254919/treatment_mCherry_hND6_sample_number_SRP254919.gprofiler2.GO:CC.sub_enriched_pathways.png",
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"plots/gprofiler2/treatment_mCherry_hND6_sample_number_SRP254919/treatment_mCherry_hND6_sample_number_SRP254919.gprofiler2.GO:MF.sub_enriched_pathways.png",
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"plots/gprofiler2/treatment_mCherry_hND6_sample_number_SRP254919/treatment_mCherry_hND6_sample_number_SRP254919.gprofiler2.gostplot.html",
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"plots/gprofiler2/treatment_mCherry_hND6_sample_number_SRP254919/treatment_mCherry_hND6_sample_number_SRP254919.gprofiler2.gostplot.png",
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"plots/immunedeconv",
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"plots/immunedeconv/SRP254919.plot1_stacked_bar_chart.png",
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"plots/immunedeconv/SRP254919.plot2_points_with_facets.png",
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"tables/gprofiler2/treatment_mCherry_hND6__SRP254919",
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"tables/gprofiler2/treatment_mCherry_hND6__SRP254919/treatment_mCherry_hND6__SRP254919.gprofiler2.all_enriched_pathways.tsv",
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"tables/gprofiler2/treatment_mCherry_hND6_sample_number_SRP254919",
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"tables/gprofiler2/treatment_mCherry_hND6_sample_number_SRP254919/treatment_mCherry_hND6_sample_number_SRP254919.gprofiler2.GO:CC.sub_enriched_pathways.tsv",
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"tables/gprofiler2/treatment_mCherry_hND6_sample_number_SRP254919/treatment_mCherry_hND6_sample_number_SRP254919.gprofiler2.GO:MF.sub_enriched_pathways.tsv",
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"tables/gprofiler2/treatment_mCherry_hND6_sample_number_SRP254919/treatment_mCherry_hND6_sample_number_SRP254919.gprofiler2.all_enriched_pathways.tsv",
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"tables/immunedeconv",
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"tables/immunedeconv/SRP254919.deconvolution_results.tsv",
@@ -124,17 +132,19 @@
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"treatment_mCherry_hND6_sample_number_SRP254919.deseq2.results.tsv:md5,3c827ffb53fe7dab8f13f0ef89a3da06",
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"treatment_mCherry_hND6_sample_number_SRP254919.deseq2.results_filtered.tsv:md5,c88d36f46f7d8a4dd8c169c249f50540",
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"treatment_mCherry_hND6__SRP254919.gprofiler2.all_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
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"treatment_mCherry_hND6_sample_number_SRP254919.gprofiler2.all_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
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"treatment_mCherry_hND6_sample_number_SRP254919.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,a7127a9491097019d3d6bb53cb00ec8e",
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"treatment_mCherry_hND6_sample_number_SRP254919.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,fc811363bc5cd3196d88906a06e20419",
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"treatment_mCherry_hND6_sample_number_SRP254919.gprofiler2.all_enriched_pathways.tsv:md5,3b069b57f1043fa5b700abeec0b28e73",
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"SRP254919.deconvolution_results.tsv:md5,3d7ed4550a0da2f63fcfd2e74605e7a3",
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"all.normalised_counts.tsv:md5,f3ef0fb48f97afde2b5122b72dc4dcc4",
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"all.vst.tsv:md5,ae82509f76ed01ad0d041d1a62aef703"
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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "25.04.6"
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"timestamp": "2025-06-17T09:59:11.644008654"
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"timestamp": "2025-09-04T13:35:37.380261016"
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},
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"Test profile - deseq2": {
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"content": [
@@ -325,9 +335,9 @@
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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "25.04.3"
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"timestamp": "2025-06-17T09:55:48.476497111"
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"timestamp": "2025-09-19T08:54:02.57428995"
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},
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"Test profile - gsea": {
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"content": [
@@ -518,7 +528,7 @@
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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "25.04.6"
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},
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"timestamp": "2025-06-17T09:57:08.6693888"
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},

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