From 5b9488375d1e2efbd8a8fe78b982905e85aa701c Mon Sep 17 00:00:00 2001 From: WackerO Date: Tue, 29 Oct 2024 11:09:37 +0100 Subject: [PATCH 01/41] removed gprofiler colons from docs --- docs/usage.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 3909b0e9..7364d837 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -286,16 +286,16 @@ Currently, two tools can be used to do gene set enrichment analysis. --gene_sets_files gene_sets.gmt ``` -### g:Profiler +### gProfiler2 -The [gprofiler2](https://cran.r-project.org/web/packages/gprofiler2/vignettes/gprofiler2.html) package can be used to test which pathways are enriched in the sets of differential genes produced by the the DESeq2 or limma modules. It is an R interface for the g:Profiler webtool. In the simplest form, this feature can be enabled with the parameters from the following example: +The [gprofiler2](https://cran.r-project.org/web/packages/gprofiler2/vignettes/gprofiler2.html) package can be used to test which pathways are enriched in the sets of differential genes produced by the the DESeq2 or limma modules. It is an R interface for the gprofiler webtool. In the simplest form, this feature can be enabled with the parameters from the following example: ```bash --gprofiler2_run true \ --gprofiler2_organism mmusculus ``` -If gene sets have been specified to the workflow via `--gene_sets_files` these are used by default. Specifying `--gprofiler2_organism` (mmusculus for Mus musculus, hsapiens for Homo sapiens etc.) will override those gene sets with g:profiler's own for the relevant species. `--gprofiler2_token` will override both options and use gene sets from a previous g:profiler run. +If gene sets have been specified to the workflow via `--gene_sets_files` these are used by default. Specifying `--gprofiler2_organism` (mmusculus for Mus musculus, hsapiens for Homo sapiens etc.) will override those gene sets with gprofiler's own for the relevant species. `--gprofiler2_token` will override both options and use gene sets from a previous gprofiler run. By default the analysis will be run with a background list of genes that passed the abundance filter (i.e. those genes that actually had some expression); see for example https://doi.org/10.1186/s13059-015-0761-7 for why this is advisable. You can provide your own background list with `--gprofiler2_background_file background.txt`or if you want to not use any background, set `--gprofiler2_background_file false`. From 1b35f8925f348828e2c7d8b8753dc1fd166a4fe6 Mon Sep 17 00:00:00 2001 From: WackerO Date: Tue, 29 Oct 2024 11:11:31 +0100 Subject: [PATCH 02/41] changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7b4f45fb..15f6c833 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Fixed +- [[#330](https://github.com/nf-core/differentialabundance/pull/330)] - Fixed broken docs by removing g:profiler colons ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords)) - [[#304](https://github.com/nf-core/differentialabundance/pull/304)] - Removed TXT file options from nextflow_schema where they are equivalent to TSV to make the input files clearer ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords)) - [[#299](https://github.com/nf-core/differentialabundance/pull/299)] - Add exclusions for 3.0.1 template update ([@pinin4fjords](https://github.com/pinin4fjords)) - [[#289](https://github.com/nf-core/differentialabundance/pull/289)] - Fix missing ch_gene_sets default for gprofiler2 ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords)) From c231474fe6c5f247a7bd04a1e12be1447c20cf9d Mon Sep 17 00:00:00 2001 From: davidecarlson Date: Tue, 29 Oct 2024 11:18:37 -0400 Subject: [PATCH 03/41] add additional reference to wiki article for MAD --- assets/differentialabundance_report.Rmd | 2 +- nextflow_schema.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/assets/differentialabundance_report.Rmd b/assets/differentialabundance_report.Rmd index 7bf41c12..acd94dca 100644 --- a/assets/differentialabundance_report.Rmd +++ b/assets/differentialabundance_report.Rmd @@ -726,7 +726,7 @@ iv_min_group_sizes <- unlist(lapply(informative_variables, function(x) min(table if (any(iv_min_group_sizes > 2)){ cat("\n### Outlier detection {.tabset}\n") - cat("\nOutlier detection based on [median absolute deviation](https://wiki.arrayserver.com/wiki/index.php?title=CorrelationQC.pdf) was undertaken, the outlier scoring is plotted below.\n") + cat("\nOutlier detection based on [median absolute deviation](https://wiki.arrayserver.com/wiki/index.php?title=CorrelationQC.pdf) was undertaken, the outlier scoring is plotted below. For more on MAD, see [this wiki article](https://en.wikipedia.org/wiki/Median_absolute_deviation).\n") } foo <- lapply(informative_variables[iv_min_group_sizes > 2], function(iv){ diff --git a/nextflow_schema.json b/nextflow_schema.json index 7e329647..3c0df50d 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -373,7 +373,7 @@ "exploratory_mad_threshold": { "type": "integer", "default": -5, - "help_text": "MAD = median absolute deviation. A threshold on this value is used to define observations (samples) as outliers, or not, in exploratory plots. Based on the definition at https://wiki.arrayserver.com/wiki/index.php?title=CorrelationQC.pdf. ", + "help_text": "MAD = median absolute deviation. A threshold on this value is used to define observations (samples) as outliers, or not, in exploratory plots. Based on the definition at https://wiki.arrayserver.com/wiki/index.php?title=CorrelationQC.pdf. For more on MAD, see https://en.wikipedia.org/wiki/Median_absolute_deviation.", "description": "Threshold on MAD score for outlier identification", "fa_icon": "fas fa-angry" }, From 37f7a1c3a09037a32e6f1f8742aae3e71a5b0ae8 Mon Sep 17 00:00:00 2001 From: Dave Carlson Date: Mon, 4 Nov 2024 08:31:12 -0500 Subject: [PATCH 04/41] Update assets/differentialabundance_report.Rmd Co-authored-by: WackerO <43847497+WackerO@users.noreply.github.com> --- assets/differentialabundance_report.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/assets/differentialabundance_report.Rmd b/assets/differentialabundance_report.Rmd index acd94dca..6a9d8cc5 100644 --- a/assets/differentialabundance_report.Rmd +++ b/assets/differentialabundance_report.Rmd @@ -726,7 +726,7 @@ iv_min_group_sizes <- unlist(lapply(informative_variables, function(x) min(table if (any(iv_min_group_sizes > 2)){ cat("\n### Outlier detection {.tabset}\n") - cat("\nOutlier detection based on [median absolute deviation](https://wiki.arrayserver.com/wiki/index.php?title=CorrelationQC.pdf) was undertaken, the outlier scoring is plotted below. For more on MAD, see [this wiki article](https://en.wikipedia.org/wiki/Median_absolute_deviation).\n") + cat("\nOutlier detection based on [median absolute deviation](https://archive.ph/o3thZ) was undertaken, the outlier scoring is plotted below. For more on MAD, see [this wiki article](https://en.wikipedia.org/wiki/Median_absolute_deviation).\n") } foo <- lapply(informative_variables[iv_min_group_sizes > 2], function(iv){ From acdcfed0ad4702c5b8a4598b6f8a686bab9cb323 Mon Sep 17 00:00:00 2001 From: Dave Carlson Date: Mon, 4 Nov 2024 08:31:33 -0500 Subject: [PATCH 05/41] Update nextflow_schema.json Co-authored-by: WackerO <43847497+WackerO@users.noreply.github.com> --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 3c0df50d..3fc76360 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -373,7 +373,7 @@ "exploratory_mad_threshold": { "type": "integer", "default": -5, - "help_text": "MAD = median absolute deviation. A threshold on this value is used to define observations (samples) as outliers, or not, in exploratory plots. Based on the definition at https://wiki.arrayserver.com/wiki/index.php?title=CorrelationQC.pdf. For more on MAD, see https://en.wikipedia.org/wiki/Median_absolute_deviation.", + "help_text": "MAD = median absolute deviation. A threshold on this value is used to define observations (samples) as outliers, or not, in exploratory plots. Based on the definition at https://archive.ph/o3thZ. For more on MAD, see https://en.wikipedia.org/wiki/Median_absolute_deviation.", "description": "Threshold on MAD score for outlier identification", "fa_icon": "fas fa-angry" }, From e1620b180c2a620ae97a4fc36943a5d971fb0727 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Thu, 7 Nov 2024 16:35:55 +0000 Subject: [PATCH 06/41] add nf-test --- .gitignore | 1 + nf-test.config | 20 +++++ tests/.nftignore | 10 +++ tests/test.nf.test | 35 +++++++++ tests/test.nf.test.snap | 160 ++++++++++++++++++++++++++++++++++++++++ 5 files changed, 226 insertions(+) create mode 100644 nf-test.config create mode 100644 tests/.nftignore create mode 100644 tests/test.nf.test create mode 100644 tests/test.nf.test.snap diff --git a/.gitignore b/.gitignore index a42ce016..776b82fe 100644 --- a/.gitignore +++ b/.gitignore @@ -7,3 +7,4 @@ testing/ testing* *.pyc null/ +.nf-test diff --git a/nf-test.config b/nf-test.config new file mode 100644 index 00000000..2884650d --- /dev/null +++ b/nf-test.config @@ -0,0 +1,20 @@ +config { + // location for all nf-tests + testsDir "tests" + + // nf-test directory including temporary files for each test + workDir ".nf-test" + + // location of library folder that is added automatically to the classpath + libDir "tests/pipeline/lib/" + + // location of an optional nextflow.config file specific for executing tests + configFile "nextflow.config" + + // run all test with the defined docker profile from the main nextflow.config + profile "docker" + + plugins { + load "nft-utils@0.0.3" + } +} diff --git a/tests/.nftignore b/tests/.nftignore new file mode 100644 index 00000000..874ba015 --- /dev/null +++ b/tests/.nftignore @@ -0,0 +1,10 @@ +pipeline_info/*.{html,json,txt,yml} +report/gsea/**/*.symbols.pvalues_vs_nes_plot.png +report/gsea/**/*.symbols.gset_rnd_es_dist_5.png +report/gsea/**/*butterfly_plot.png +report/gsea/**/*.gsea_report_for_hND6.tsv +report/gsea/**/*.symbols.Gsea.rpt +report/gsea/**/*.html +report/*.html +report/*.zip +*html diff --git a/tests/test.nf.test b/tests/test.nf.test new file mode 100644 index 00000000..78c0e476 --- /dev/null +++ b/tests/test.nf.test @@ -0,0 +1,35 @@ +nextflow_pipeline { + + name "Test Workflow main.nf - DIFFERENTIALABUNDANCE" + script "../main.nf" + profile "+test" + tag "differentialabundance" + tag "pipeline" + + test("Should run differentialabundance pipeline with test profile") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } +} diff --git a/tests/test.nf.test.snap b/tests/test.nf.test.snap new file mode 100644 index 00000000..37a4395e --- /dev/null +++ b/tests/test.nf.test.snap @@ -0,0 +1,160 @@ +{ + "Should run differentialabundance pipeline with test profile": { + "content": [ + 21, + [ + "other", + "other/deseq2", + "other/deseq2/treatment_mCherry_hND6_.dds.rld.rds", + "other/deseq2/treatment_mCherry_hND6_.deseq2.sizefactors.tsv", + "other/deseq2/treatment_mCherry_hND6_sample_number.dds.rld.rds", + "other/deseq2/treatment_mCherry_hND6_sample_number.deseq2.sizefactors.tsv", + "pipeline_info", + "pipeline_info/collated_versions.yml", + "plots", + "plots/differential", + "plots/differential/treatment_mCherry_hND6_", + "plots/differential/treatment_mCherry_hND6_/png", + "plots/differential/treatment_mCherry_hND6_/png/volcano.png", + "plots/differential/treatment_mCherry_hND6_sample_number", 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], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-07T16:30:24.403732283" + } +} \ No newline at end of file From cac778345e68ddfcd9a5c857357326ea7e370154 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Thu, 7 Nov 2024 17:23:54 +0000 Subject: [PATCH 07/41] add more tests and snapshots --- .gitignore | 1 + tests/test.nf.test | 4 +- tests/test.nf.test.snap | 4 +- tests/test_affy.nf.test | 35 +++ tests/test_affy.nf.test.snap | 438 +++++++++++++++++++++++++++ tests/test_maxquant.nf.test | 35 +++ tests/test_maxquant.nf.test.snap | 152 ++++++++++ tests/test_nogtf.nf.test | 35 +++ tests/test_nogtf.nf.test.snap | 88 ++++++ tests/test_rnaseq_limma.nf.test | 35 +++ tests/test_rnaseq_limma.nf.test.snap | 151 +++++++++ tests/test_soft.nf.test | 35 +++ tests/test_soft.nf.test.snap | 76 +++++ 13 files changed, 1085 insertions(+), 4 deletions(-) create mode 100644 tests/test_affy.nf.test create mode 100644 tests/test_affy.nf.test.snap create mode 100644 tests/test_maxquant.nf.test create mode 100644 tests/test_maxquant.nf.test.snap create mode 100644 tests/test_nogtf.nf.test create mode 100644 tests/test_nogtf.nf.test.snap create mode 100644 tests/test_rnaseq_limma.nf.test create mode 100644 tests/test_rnaseq_limma.nf.test.snap create mode 100644 tests/test_soft.nf.test create mode 100644 tests/test_soft.nf.test.snap diff --git a/.gitignore b/.gitignore index 776b82fe..9e307203 100644 --- a/.gitignore +++ b/.gitignore @@ -8,3 +8,4 @@ testing* *.pyc null/ .nf-test +.nf-test.log diff --git a/tests/test.nf.test b/tests/test.nf.test index 78c0e476..908e7aec 100644 --- a/tests/test.nf.test +++ b/tests/test.nf.test @@ -3,10 +3,10 @@ nextflow_pipeline { name "Test Workflow main.nf - DIFFERENTIALABUNDANCE" script "../main.nf" profile "+test" - tag "differentialabundance" + tag "test" tag "pipeline" - test("Should run differentialabundance pipeline with test profile") { + test("Test profile") { when { params { diff --git a/tests/test.nf.test.snap b/tests/test.nf.test.snap index 37a4395e..46831c42 100644 --- a/tests/test.nf.test.snap +++ b/tests/test.nf.test.snap @@ -1,5 +1,5 @@ { - "Should run differentialabundance pipeline with test profile": { + "Test profile": { "content": [ 21, [ @@ -155,6 +155,6 @@ "nf-test": "0.9.0", "nextflow": "24.10.0" }, - "timestamp": "2024-11-07T16:30:24.403732283" + "timestamp": "2024-11-07T17:19:02.508819768" } } \ No newline at end of file diff --git a/tests/test_affy.nf.test b/tests/test_affy.nf.test new file mode 100644 index 00000000..b2f651f8 --- /dev/null +++ b/tests/test_affy.nf.test @@ -0,0 +1,35 @@ +nextflow_pipeline { + + name "Test Workflow main.nf - DIFFERENTIALABUNDANCE" + script "../main.nf" + profile "+test_affy" + tag "affy" + tag "pipeline" + + test("Test affy profile") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } +} diff --git a/tests/test_affy.nf.test.snap b/tests/test_affy.nf.test.snap new file mode 100644 index 00000000..ea012448 --- /dev/null +++ b/tests/test_affy.nf.test.snap @@ -0,0 +1,438 @@ +{ + "Test affy profile": { + "content": [ + 16, + [ + "other", + "other/affy", + "other/affy/raw.eset.rds", + "other/limma", + "other/limma/phenotype_uninvolved_lesional.MArrayLM.limma.rds", + "pipeline_info", + "pipeline_info/collated_versions.yml", + 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"versions.yml:md5,892774f9d56ba10c8646736b7f777ecc", + "hgu133plus2.annotation.tsv:md5,f2b82ef12b2a2e8e575de06766583d96", + "phenotype_uninvolved_lesional.limma.results.tsv:md5,686e871be0f1b435e161f84f6518cfc3", + "phenotype_uninvolved_lesional.limma.results_filtered.tsv:md5,f7f9f8914173ecb4a9af2d35afd62aae", + "normalised.matrix.tsv:md5,68d849e627d86095cfb48eba81c09853", + "raw.matrix.tsv:md5,ea5cccce75c3a9a5d2aab3e3a19910ad", + "GSM1229341_Gudjohnsson_001_6690_PP.CEL.gz:md5,259d0908211a071351450f366fd51cad", + "GSM1229342_Gudjohnsson_002_6690_PN.CEL.gz:md5,31cc2b8b26e210760b8ebd4b304b52ba", + "GSM1229343_Gudjohnsson_003_7450_PN.CEL.gz:md5,713a3ca75a883cbff6da0be7bd251422", + "GSM1229344_Gudjohnsson_004_7450_PP.CEL.gz:md5,6f9b8815282bd0fd51c575145acf08cb", + "GSM1229345_Gudjohnsson_005_7912_PP.CEL.gz:md5,69c709ce4ede2b85c931a903b3805d60", + "GSM1229346_Gudjohnsson_006_7912_PN.CEL.gz:md5,e05ae9fab96c299416878c4cbbd74327", + "GSM1229347_Gudjohnsson_007_8470_PP.CEL.gz:md5,951ce488dd3baf0141e6eabc233bd8c7", + "GSM1229348_Gudjohnsson_008_8470_PN.CEL.gz:md5,ec5129e035badf3b670178d53e24f0cc" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-07T16:54:13.324385664" + } +} \ No newline at end of file diff --git a/tests/test_maxquant.nf.test b/tests/test_maxquant.nf.test new file mode 100644 index 00000000..cb2c9556 --- /dev/null +++ b/tests/test_maxquant.nf.test @@ -0,0 +1,35 @@ +nextflow_pipeline { + + name "Test Workflow main.nf - DIFFERENTIALABUNDANCE" + script "../main.nf" + profile "+test_maxquant" + tag "maxquant" + tag "pipeline" + + test("Test maxquant profile") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } +} diff --git a/tests/test_maxquant.nf.test.snap b/tests/test_maxquant.nf.test.snap new file mode 100644 index 00000000..28acf7e4 --- /dev/null +++ b/tests/test_maxquant.nf.test.snap @@ -0,0 +1,152 @@ +{ + "Test maxquant profile": { + "content": [ + 20, + [ + "other", + "other/limma", + "other/limma/fakebatch_fakeBatch_b1_b2.MArrayLM.limma.rds", + "other/limma/genotype_celltype_t1_FoB.MArrayLM.limma.rds", + "other/limma/genotype_celltype_t1_MZ_fakeBatch.MArrayLM.limma.rds", + "other/limma/genotype_celltype_t1_t2.MArrayLM.limma.rds", + "other/proteus", + "other/proteus/Celltype", + "other/proteus/Celltype/normalizeMedian.normalized_proteingroups.rds", + "other/proteus/Celltype/raw_proteingroups.rds", + "other/proteus/R_sessionInfo.log", + "other/proteus/fakeBatch", + "other/proteus/fakeBatch/normalizeMedian.normalized_proteingroups.rds", + "other/proteus/fakeBatch/raw_proteingroups.rds", + "pipeline_info", + "pipeline_info/collated_versions.yml", + "plots", + "plots/differential", + "plots/differential/fakebatch_fakeBatch_b1_b2", + "plots/differential/fakebatch_fakeBatch_b1_b2/png", + "plots/differential/fakebatch_fakeBatch_b1_b2/png/volcano.png", + "plots/differential/genotype_celltype_t1_FoB", + "plots/differential/genotype_celltype_t1_FoB/png", + "plots/differential/genotype_celltype_t1_FoB/png/volcano.png", + "plots/differential/genotype_celltype_t1_MZ_fakeBatch", + "plots/differential/genotype_celltype_t1_MZ_fakeBatch/png", + "plots/differential/genotype_celltype_t1_MZ_fakeBatch/png/volcano.png", + "plots/differential/genotype_celltype_t1_t2", + "plots/differential/genotype_celltype_t1_t2/png", + "plots/differential/genotype_celltype_t1_t2/png/volcano.png", + "plots/differential/versions.yml", + "plots/exploratory", + "plots/exploratory/Celltype", + "plots/exploratory/Celltype/png", + "plots/exploratory/Celltype/png/boxplot.png", + "plots/exploratory/Celltype/png/density.png", + "plots/exploratory/Celltype/png/mad_correlation.png", + "plots/exploratory/Celltype/png/pca2d.png", + "plots/exploratory/Celltype/png/pca3d.png", + "plots/exploratory/Celltype/png/sample_dendrogram.png", + "plots/exploratory/fakeBatch", + "plots/exploratory/fakeBatch/png", + "plots/exploratory/fakeBatch/png/boxplot.png", + "plots/exploratory/fakeBatch/png/density.png", + "plots/exploratory/fakeBatch/png/mad_correlation.png", + "plots/exploratory/fakeBatch/png/pca2d.png", + "plots/exploratory/fakeBatch/png/pca3d.png", + "plots/exploratory/fakeBatch/png/sample_dendrogram.png", + "plots/exploratory/versions.yml", + "plots/proteus", + "plots/proteus/Celltype", + "plots/proteus/Celltype/normalizeMedian.normalized_dendrogram.png", + "plots/proteus/Celltype/normalizeMedian.normalized_distributions.png", + "plots/proteus/Celltype/normalizeMedian.normalized_mean_variance_relationship.png", + "plots/proteus/Celltype/raw_distributions.png", + "plots/proteus/fakeBatch", + "plots/proteus/fakeBatch/normalizeMedian.normalized_dendrogram.png", + "plots/proteus/fakeBatch/normalizeMedian.normalized_distributions.png", + "plots/proteus/fakeBatch/normalizeMedian.normalized_mean_variance_relationship.png", + "plots/proteus/fakeBatch/raw_distributions.png", + "plots/qc", + "plots/qc/fakebatch_fakeBatch_b1_b2.limma.mean_difference.png", + "plots/qc/genotype_celltype_t1_FoB.limma.mean_difference.png", + "plots/qc/genotype_celltype_t1_MZ_fakeBatch.limma.mean_difference.png", + "plots/qc/genotype_celltype_t1_t2.limma.mean_difference.png", + "report", + "report/PXD043349.html", + "report/PXD043349.zip", + "tables", + "tables/differential", + "tables/differential/fakebatch_fakeBatch_b1_b2.limma.results.tsv", + "tables/differential/fakebatch_fakeBatch_b1_b2.limma.results_filtered.tsv", + "tables/differential/genotype_celltype_t1_FoB.limma.results.tsv", + "tables/differential/genotype_celltype_t1_FoB.limma.results_filtered.tsv", + "tables/differential/genotype_celltype_t1_MZ_fakeBatch.limma.results.tsv", + "tables/differential/genotype_celltype_t1_MZ_fakeBatch.limma.results_filtered.tsv", + "tables/differential/genotype_celltype_t1_t2.limma.results.tsv", + "tables/differential/genotype_celltype_t1_t2.limma.results_filtered.tsv", + "tables/proteus", + "tables/proteus/Celltype", + "tables/proteus/Celltype/normalizeMedian.normalized_proteingroups_tab.tsv", + "tables/proteus/Celltype/raw_proteingroups_tab.tsv", + "tables/proteus/fakeBatch", + "tables/proteus/fakeBatch/normalizeMedian.normalized_proteingroups_tab.tsv", + "tables/proteus/fakeBatch/raw_proteingroups_tab.tsv" + ], + [ + "fakebatch_fakeBatch_b1_b2.MArrayLM.limma.rds:md5,f321bf1e4fd44827810df9a9c38776d6", + "genotype_celltype_t1_FoB.MArrayLM.limma.rds:md5,4f0cb9d82aa3c0464cee5eca69248589", + "genotype_celltype_t1_MZ_fakeBatch.MArrayLM.limma.rds:md5,2021a25cc716b10830ff6851044b6b9d", + "genotype_celltype_t1_t2.MArrayLM.limma.rds:md5,34cc962386f20c6e001ab28f035df781", + "normalizeMedian.normalized_proteingroups.rds:md5,da660b225f066a1e87bf8bb4196adcc6", + "raw_proteingroups.rds:md5,0b38726c41e7b32213e5e15380c29612", + "R_sessionInfo.log:md5,411badddf7904da0ed1de02b544109d2", + "normalizeMedian.normalized_proteingroups.rds:md5,6f7def9ce31c8ee07f649675db394848", + "raw_proteingroups.rds:md5,daef7d25977a1628870dee75e2977ee3", + "volcano.png:md5,3d64aa38b9c321f1162565a28d254bd1", + "volcano.png:md5,2497d3bd1e925d358b5856a21209f4bc", + "volcano.png:md5,1b28d0983a895d0619c470553a1be47f", + "volcano.png:md5,198730d78767da2e46ce6e1d25f52e64", + "versions.yml:md5,b20728a34a3537e339078bbeaababee9", + "boxplot.png:md5,17074b29c8babf56c5b884c13429c81e", + "density.png:md5,245843935e441c32d69b788d0cdd9ef8", + "mad_correlation.png:md5,e2033c95c4c5b3d695d65158a6a246e4", + "pca2d.png:md5,50ff3bd8c8de40f32f078fe879c72d55", + "pca3d.png:md5,c3ced5600509551d5e0410019c717445", + "sample_dendrogram.png:md5,49bcc85503e49cb9da71e86973db3263", + "boxplot.png:md5,bb306103d822eecc37c29bb07674d29f", + "density.png:md5,a27331aa3cb96242140cba1f57a18215", + "mad_correlation.png:md5,e14dd0b2ab73187658b386dfc6227d37", + "pca2d.png:md5,ed7f1342d245d5764898b637a6530c8d", + "pca3d.png:md5,dcedf79d5795c48a57117a2279dd4a0e", + "sample_dendrogram.png:md5,bacaf55f4f5863992ce7c166cde9c5b9", + "versions.yml:md5,9c47cbf6f2f30c711eb57fff84ea3736", + "normalizeMedian.normalized_dendrogram.png:md5,6bf22a6e3aba7d3c53dc80d3bbd2bb27", + "normalizeMedian.normalized_distributions.png:md5,39b6f96288b8cd2e7dd2d02f424d6d78", + "normalizeMedian.normalized_mean_variance_relationship.png:md5,4ed879017fcbe0ea8279bd362ac0d9bd", 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"genotype_celltype_t1_FoB.limma.results.tsv:md5,990fa0b6a9618bcb03d4c6726f0d518a", + "genotype_celltype_t1_FoB.limma.results_filtered.tsv:md5,941463996b8790278d7062a48fbc3419", + "genotype_celltype_t1_MZ_fakeBatch.limma.results.tsv:md5,a0cd63a2f76307016904a4463e3b1791", + "genotype_celltype_t1_MZ_fakeBatch.limma.results_filtered.tsv:md5,b3120632d1f653e97d18342089157930", + "genotype_celltype_t1_t2.limma.results.tsv:md5,8e6f5de58fc478aa954350fc159a9b57", + "genotype_celltype_t1_t2.limma.results_filtered.tsv:md5,9db67d9283e7fb2f4f604fd63ec40e4d", + "normalizeMedian.normalized_proteingroups_tab.tsv:md5,154fcd8d23409981b897d153e7b7e34e", + "raw_proteingroups_tab.tsv:md5,33a8791f84c676ea1aea4842231acb6a", + "normalizeMedian.normalized_proteingroups_tab.tsv:md5,154fcd8d23409981b897d153e7b7e34e", + "raw_proteingroups_tab.tsv:md5,33a8791f84c676ea1aea4842231acb6a" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-07T16:57:00.079425408" + } +} \ No newline at end of file diff --git a/tests/test_nogtf.nf.test b/tests/test_nogtf.nf.test new file mode 100644 index 00000000..6ddef9cd --- /dev/null +++ b/tests/test_nogtf.nf.test @@ -0,0 +1,35 @@ +nextflow_pipeline { + + name "Test Workflow main.nf - DIFFERENTIALABUNDANCE" + script "../main.nf" + profile "+test_nogtf" + tag "nogtf" + tag "pipeline" + + test("Test no gtf profile") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } +} diff --git a/tests/test_nogtf.nf.test.snap b/tests/test_nogtf.nf.test.snap new file mode 100644 index 00000000..c8dfb7d9 --- /dev/null +++ b/tests/test_nogtf.nf.test.snap @@ -0,0 +1,88 @@ +{ + "Test no gtf profile": { + "content": [ + 13, + [ + "other", + "other/deseq2", + "other/deseq2/treatment_mCherry_hND6_.dds.rld.rds", + "other/deseq2/treatment_mCherry_hND6_.deseq2.sizefactors.tsv", + "other/deseq2/treatment_mCherry_hND6_sample_number.dds.rld.rds", + "other/deseq2/treatment_mCherry_hND6_sample_number.deseq2.sizefactors.tsv", + "pipeline_info", + "pipeline_info/collated_versions.yml", + "plots", + "plots/differential", + "plots/differential/treatment_mCherry_hND6_", + "plots/differential/treatment_mCherry_hND6_/png", + "plots/differential/treatment_mCherry_hND6_/png/volcano.png", + "plots/differential/treatment_mCherry_hND6_sample_number", + 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"treatment_mCherry_hND6_sample_number.deseq2.results.tsv:md5,02b1c8f3c2987b0cb1a64913dd90bf26", + "treatment_mCherry_hND6_sample_number.deseq2.results_filtered.tsv:md5,1e1c8edb0aa5acee308bc1fc81d1aa16", + "all.normalised_counts.tsv:md5,e960aa685547a3ea778523da84fae136", + "all.vst.tsv:md5,ea4e437ee57b2c5ef8c19d427656e3c6" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-07T16:59:16.942778374" + } +} \ No newline at end of file diff --git a/tests/test_rnaseq_limma.nf.test b/tests/test_rnaseq_limma.nf.test new file mode 100644 index 00000000..09b4b20c --- /dev/null +++ b/tests/test_rnaseq_limma.nf.test @@ -0,0 +1,35 @@ +nextflow_pipeline { + + name "Test Workflow main.nf - DIFFERENTIALABUNDANCE" + script "../main.nf" + profile "+test_rnaseq_limma" + tag "rnaseq_limma" + tag "pipeline" + + test("Test rnaseq limma profile") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } +} diff --git a/tests/test_rnaseq_limma.nf.test.snap b/tests/test_rnaseq_limma.nf.test.snap new file mode 100644 index 00000000..50575faa --- /dev/null +++ b/tests/test_rnaseq_limma.nf.test.snap @@ -0,0 +1,151 @@ +{ + "Test rnaseq limma profile": { + "content": [ + 20, + [ + "other", + "other/limma", + "other/limma/treatment_mCherry_hND6_.MArrayLM.limma.rds", + 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"treatment_mCherry_hND6_sample_number.mh.all.v2022.1.Mm.symbols.ranked_list_corr_2.png:md5,35c67dd6865094465ffbce6a237d46dc", + "app.R:md5,bedcfc45b6cdcc2b8fe3627987e2b17a", + "data.rds:md5,8af09cffb7fdf11b0ed25cf502bdcae8", + "versions.yml:md5,892774f9d56ba10c8646736b7f777ecc", + "Mus_musculus.anno.tsv:md5,c1d7f21e64bd00f845ec6545c123a1fb", + "treatment_mCherry_hND6_.limma.results.tsv:md5,26df55a9c0fd182977396f75337d5fc4", + "treatment_mCherry_hND6_.limma.results_filtered.tsv:md5,0bfc9215edc6aad064c3ce6abc81bfce", + "treatment_mCherry_hND6_sample_number.limma.results.tsv:md5,2a3937bfc95a1d0a0cbed1f2da4b0bd2", + "treatment_mCherry_hND6_sample_number.limma.results_filtered.tsv:md5,0bfc9215edc6aad064c3ce6abc81bfce" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-07T17:01:26.589438715" + } +} \ No newline at end of file diff --git a/tests/test_soft.nf.test b/tests/test_soft.nf.test new file mode 100644 index 00000000..5c09e648 --- /dev/null +++ b/tests/test_soft.nf.test @@ -0,0 +1,35 @@ +nextflow_pipeline { + + name "Test Workflow main.nf - DIFFERENTIALABUNDANCE" + script "../main.nf" + profile "+test_soft" + tag "soft" + tag "pipeline" + + test("Test soft profile") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } +} diff --git a/tests/test_soft.nf.test.snap b/tests/test_soft.nf.test.snap new file mode 100644 index 00000000..dd65cd41 --- /dev/null +++ b/tests/test_soft.nf.test.snap @@ -0,0 +1,76 @@ +{ + "Test soft profile": { + "content": [ + 10, + [ + "other", + "other/affy", + "other/affy/normalised.eset.rds", + "other/limma", + "other/limma/phenotype_uninvolved_lesional.MArrayLM.limma.rds", + "pipeline_info", + "pipeline_info/collated_versions.yml", + "plots", + "plots/differential", + "plots/differential/phenotype_uninvolved_lesional", + "plots/differential/phenotype_uninvolved_lesional/png", + "plots/differential/phenotype_uninvolved_lesional/png/volcano.png", + "plots/differential/versions.yml", + "plots/exploratory", + "plots/exploratory/phenotype", + "plots/exploratory/phenotype/png", + "plots/exploratory/phenotype/png/boxplot.png", + "plots/exploratory/phenotype/png/density.png", + "plots/exploratory/phenotype/png/mad_correlation.png", + "plots/exploratory/phenotype/png/pca2d.png", + "plots/exploratory/phenotype/png/pca3d.png", + "plots/exploratory/phenotype/png/sample_dendrogram.png", + "plots/exploratory/versions.yml", + "plots/qc", + "plots/qc/phenotype_uninvolved_lesional.limma.mean_difference.png", + "report", + "report/study.html", + "report/study.zip", + "shinyngs_app", + "shinyngs_app/study", + "shinyngs_app/study/app.R", + "shinyngs_app/study/data.rds", + "shinyngs_app/versions.yml", + "tables", + "tables/annotation", + "tables/annotation/normalised.annotation.tsv", + "tables/differential", + "tables/differential/phenotype_uninvolved_lesional.limma.results.tsv", + "tables/differential/phenotype_uninvolved_lesional.limma.results_filtered.tsv", + "tables/processed_abundance", + "tables/processed_abundance/normalised.matrix.tsv" + ], + [ + "normalised.eset.rds:md5,7f17b964d5a7b369767910635dfa23d7", + "phenotype_uninvolved_lesional.MArrayLM.limma.rds:md5,eecc9b0267ce9a5d3a1330da7fbce4cc", + "volcano.png:md5,18e35512a52ff82be16cc14330c1ac89", + "versions.yml:md5,b20728a34a3537e339078bbeaababee9", + "boxplot.png:md5,4d366be0ef28c1aaabebf1529e2b9dc0", + "density.png:md5,09b20c49c9f479fd5c36630f86ce8384", + "mad_correlation.png:md5,60f9c0e924d52a569d976a3fb2c22a43", + "pca2d.png:md5,aad430028daa7ffa7cd6bea1c6c41d43", + "pca3d.png:md5,d32182b1005d696da648170f3bd9dbe8", + "sample_dendrogram.png:md5,b66045a3c9df5310f3241544c50f3fd1", + "versions.yml:md5,9c47cbf6f2f30c711eb57fff84ea3736", + "phenotype_uninvolved_lesional.limma.mean_difference.png:md5,570bc62fbad15b7b25eaea786a416ace", + "app.R:md5,bedcfc45b6cdcc2b8fe3627987e2b17a", + "data.rds:md5,71508ad31e0fb1b69ed569c85470f660", + "versions.yml:md5,892774f9d56ba10c8646736b7f777ecc", + "normalised.annotation.tsv:md5,40300ae222ae35fa54daf10a1b86e830", + "phenotype_uninvolved_lesional.limma.results.tsv:md5,2cfa653fffb034be4b82abf306c87bc5", + "phenotype_uninvolved_lesional.limma.results_filtered.tsv:md5,6a198c35b193bab0b3148d147c7b08e3", + "normalised.matrix.tsv:md5,230f87f91c0c1a7e2ab354200c4b978c" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-07T16:45:37.804157158" + } +} \ No newline at end of file From e6173e5bbdb94482fff3d6479c8ebe2c49be7c0a Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Thu, 7 Nov 2024 18:37:16 +0000 Subject: [PATCH 08/41] update ignore and snap --- tests/.nftignore | 3 + tests/test_affy.nf.test.snap | 167 ++++++----------------------------- 2 files changed, 32 insertions(+), 138 deletions(-) diff --git a/tests/.nftignore b/tests/.nftignore index 874ba015..7a7b5d33 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -5,6 +5,9 @@ report/gsea/**/*butterfly_plot.png report/gsea/**/*.gsea_report_for_hND6.tsv report/gsea/**/*.symbols.Gsea.rpt report/gsea/**/*.html +report/gsea/phenotype_uninvolved_lesional/**/*.png +report/gsea/**/phenotype_uninvolved_lesional.*.gsea_report_for_*.tsv report/*.html report/*.zip *html +data.rds diff --git a/tests/test_affy.nf.test.snap b/tests/test_affy.nf.test.snap index ea012448..5ced0bb0 100644 --- a/tests/test_affy.nf.test.snap +++ b/tests/test_affy.nf.test.snap @@ -43,13 +43,13 @@ "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_ALLOGRAFT_REJECTION_43.png", "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_ANDROGEN_RESPONSE.html", "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_ANDROGEN_RESPONSE.tsv", - "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_ANDROGEN_RESPONSE_94.png", + "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_ANDROGEN_RESPONSE_97.png", 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"report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_APOPTOSIS_52.png", "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_BILE_ACID_METABOLISM.html", "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_BILE_ACID_METABOLISM.tsv", "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_BILE_ACID_METABOLISM_64.png", @@ -58,13 +58,13 @@ "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_CHOLESTEROL_HOMEOSTASIS_76.png", "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_COMPLEMENT.html", 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"phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.ranked_gene_list_lesional_versus_uninvolved.tsv:md5,72dfaeff534ba9a2b32f63524e835dc4", - "phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.ranked_list_corr_2.png:md5,803a07d70d668fb670425f8da59d11e9", "app.R:md5,bedcfc45b6cdcc2b8fe3627987e2b17a", "data.rds:md5,12443200d8ebe6a8e9d5409d5592dbc9", "versions.yml:md5,892774f9d56ba10c8646736b7f777ecc", @@ -433,6 +324,6 @@ "nf-test": "0.9.0", "nextflow": "24.10.0" }, - "timestamp": "2024-11-07T16:54:13.324385664" + "timestamp": "2024-11-07T18:28:13.417448088" } } \ No newline at end of file From ee50d9d2011cfb2f0fe00e889d48386c52163996 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Thu, 7 Nov 2024 18:50:40 +0000 Subject: [PATCH 09/41] update affy test --- tests/test_affy.nf.test | 2 +- tests/test_affy.nf.test.snap | 112 +---------------------------------- 2 files changed, 2 insertions(+), 112 deletions(-) diff --git a/tests/test_affy.nf.test b/tests/test_affy.nf.test index b2f651f8..4f035ad0 100644 --- a/tests/test_affy.nf.test +++ b/tests/test_affy.nf.test @@ -16,7 +16,7 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}', 'report/gsea/phenotype_uninvolved_lesional/**/*.png']) // stable_path: All files in ${params.outdir}/ with stable content def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( diff --git a/tests/test_affy.nf.test.snap b/tests/test_affy.nf.test.snap index 5ced0bb0..c9fc3228 100644 --- a/tests/test_affy.nf.test.snap +++ b/tests/test_affy.nf.test.snap @@ -37,195 +37,85 @@ 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"report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.pos_snapshot.html", - "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.pvalues_vs_nes_plot.png", "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.ranked_gene_list_lesional_versus_uninvolved.tsv", - "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.ranked_list_corr_2.png", "shinyngs_app", "shinyngs_app/GSE50790", "shinyngs_app/GSE50790/app.R", @@ -324,6 +214,6 @@ "nf-test": "0.9.0", "nextflow": "24.10.0" }, - "timestamp": "2024-11-07T18:28:13.417448088" + "timestamp": "2024-11-07T18:45:19.680294927" } } \ No newline at end of file From a77fe9a498a7fed6acdaf1a9441e0777bac35762 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Thu, 7 Nov 2024 19:18:34 +0000 Subject: [PATCH 10/41] add sharding --- .github/workflows/ci.yml | 69 +++++++++++++++++++++++++++------------- 1 file changed, 47 insertions(+), 22 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index adae0789..9c2b982e 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,15 +1,19 @@ name: nf-core CI # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors on: - push: + pull_request: branches: - dev - pull_request: + - master release: types: [published] workflow_dispatch: env: + NFT_DIFF: "pdiff" + NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2" + NFT_VER: "0.9.2" + NFT_WORKDIR: "~" NXF_ANSI_LOG: false NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity @@ -20,39 +24,33 @@ concurrency: jobs: test: - name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_profile }} | ${{ matrix.compute_profile }})" + name: "${{ matrix.NXF_VER }} | ${{ matrix.profile }} | ${{ matrix.shard }}/6" # Only run on push if this is the nf-core dev branch (merged PRs) if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/differentialabundance') }}" runs-on: ubuntu-latest strategy: + fail-fast: false matrix: NXF_VER: - "24.04.2" - "latest-everything" - test_profile: - - "test" - - "test_nogtf" - - "test_affy" - - "test_maxquant" - - "test_soft" - - "test_rnaseq_limma" - compute_profile: - - "conda" + profile: - "docker" - "singularity" - test_name: - - "test" isMaster: - ${{ github.base_ref == 'master' }} # Exclude conda and singularity on dev exclude: - isMaster: false - compute_profile: "conda" + profile: "conda" - isMaster: false - compute_profile: "singularity" + profile: "singularity" + shard: [1, 2, 3, 4, 5, 6] steps: - name: Check out pipeline code uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + with: + fetch-depth: 0 - name: Set up Nextflow uses: nf-core/setup-nextflow@v2 @@ -60,17 +58,17 @@ jobs: version: "${{ matrix.NXF_VER }}" - name: Set up Apptainer - if: matrix.compute_profile == 'singularity' + if: matrix.profile == 'singularity' uses: eWaterCycle/setup-apptainer@main - name: Set up Singularity - if: matrix.compute_profile == 'singularity' + if: matrix.profile == 'singularity' run: | mkdir -p $NXF_SINGULARITY_CACHEDIR mkdir -p $NXF_SINGULARITY_LIBRARYDIR - name: Set up Miniconda - if: matrix.compute_profile == 'conda' + if: matrix.profile == 'conda' uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 with: miniconda-version: "latest" @@ -79,7 +77,7 @@ jobs: channels: conda-forge,bioconda - name: Set up Conda - if: matrix.compute_profile == 'conda' + if: matrix.profile == 'conda' run: | echo $(realpath $CONDA)/condabin >> $GITHUB_PATH echo $(realpath python) >> $GITHUB_PATH @@ -87,6 +85,33 @@ jobs: - name: Clean up Disk space uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.compute_profile }}" + - uses: actions/setup-python@v4 + with: + python-version: "3.11" + architecture: "x64" + + - name: Install pdiff to see diff between nf-test snapshots run: | - nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_profile }},${{ matrix.compute_profile }} --outdir ./results + python -m pip install --upgrade pip + pip install pdiff + + - uses: nf-core/setup-nf-test@v1 + with: + version: ${{ env.NFT_VER }} + + - name: Run Tests (Shard ${{ matrix.shard }}/6) + run: | + nf-test test \ + --ci \ + --shard ${{ matrix.shard }}/6 \ + --changed-since HEAD^ \ + --profile "+${{ matrix.profile }}" \ + --filter pipeline \ + --junitxml=test.xml + + - name: Publish Test Report + uses: mikepenz/action-junit-report@v3 + if: always() # always run even if the previous step fails + with: + report_paths: test.xml + annotate_only: true From bb7c0270aa0d6e59fad6f9602776c727dd7e18d6 Mon Sep 17 00:00:00 2001 From: WackerO Date: Fri, 8 Nov 2024 09:09:56 +0100 Subject: [PATCH 11/41] Fixed wrongly colored dots in report volcano --- CHANGELOG.md | 1 + assets/differentialabundance_report.Rmd | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7b4f45fb..d55b421c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Fixed +- [[#342](https://github.com/nf-core/differentialabundance/pull/342)] - Fixed incorrectly colored dots in report volcano plots for logFC thresholds <1 ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords)) - [[#304](https://github.com/nf-core/differentialabundance/pull/304)] - Removed TXT file options from nextflow_schema where they are equivalent to TSV to make the input files clearer ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords)) - [[#299](https://github.com/nf-core/differentialabundance/pull/299)] - Add exclusions for 3.0.1 template update ([@pinin4fjords](https://github.com/pinin4fjords)) - [[#289](https://github.com/nf-core/differentialabundance/pull/289)] - Fix missing ch_gene_sets default for gprofiler2 ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords)) diff --git a/assets/differentialabundance_report.Rmd b/assets/differentialabundance_report.Rmd index b13d321c..55099aa6 100644 --- a/assets/differentialabundance_report.Rmd +++ b/assets/differentialabundance_report.Rmd @@ -833,7 +833,7 @@ for (i in 1:nrow(contrasts)){ cat("\n##### ", pvt, " p values\n") pval_column <- p_value_types[[pvt]] - de_fc <- abs(full_de[[params$differential_fc_column]]) >= log2(params$differential_min_fold_change) + de_fc <- abs(full_de[[params$differential_fc_column]]) >= abs(log2(params$differential_min_fold_change)) de_fc_label <- paste("abs(logFC) >=", log2(params$differential_min_fold_change)) de_pval <- full_de[[pval_column]] <= p_value_thresholds[[pvt]] From 2dfb48c258a35694590496d13d7e8f945579017f Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Fri, 8 Nov 2024 13:12:38 +0000 Subject: [PATCH 12/41] fix ci not triggered on expected events --- .github/workflows/ci.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 9c2b982e..e927f7b1 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,12 +1,12 @@ name: nf-core CI # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors on: + push: + branches: + - dev pull_request: - branches: - - dev - - master release: - types: [published] + types: [published] workflow_dispatch: env: From 7885e2610df9f29fca9f36c65d7935305fb7ac49 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Fri, 8 Nov 2024 13:12:52 +0000 Subject: [PATCH 13/41] add unstable file to nftignore --- tests/.nftignore | 2 +- tests/test_rnaseq_limma.nf.test.snap | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/tests/.nftignore b/tests/.nftignore index 7a7b5d33..a1c812b0 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -10,4 +10,4 @@ report/gsea/**/phenotype_uninvolved_lesional.*.gsea_report_for_*.tsv report/*.html report/*.zip *html -data.rds +shinyngs_app/SRP254919/data.rds diff --git a/tests/test_rnaseq_limma.nf.test.snap b/tests/test_rnaseq_limma.nf.test.snap index 50575faa..3da2acf4 100644 --- a/tests/test_rnaseq_limma.nf.test.snap +++ b/tests/test_rnaseq_limma.nf.test.snap @@ -133,7 +133,6 @@ "treatment_mCherry_hND6_sample_number.mh.all.v2022.1.Mm.symbols.ranked_gene_list_hND6_versus_mCherry.tsv:md5,2054b247acc714589b7f1e4f25a348d8", "treatment_mCherry_hND6_sample_number.mh.all.v2022.1.Mm.symbols.ranked_list_corr_2.png:md5,35c67dd6865094465ffbce6a237d46dc", "app.R:md5,bedcfc45b6cdcc2b8fe3627987e2b17a", - "data.rds:md5,8af09cffb7fdf11b0ed25cf502bdcae8", "versions.yml:md5,892774f9d56ba10c8646736b7f777ecc", "Mus_musculus.anno.tsv:md5,c1d7f21e64bd00f845ec6545c123a1fb", "treatment_mCherry_hND6_.limma.results.tsv:md5,26df55a9c0fd182977396f75337d5fc4", @@ -146,6 +145,6 @@ "nf-test": "0.9.0", "nextflow": "24.10.0" }, - "timestamp": "2024-11-07T17:01:26.589438715" + "timestamp": "2024-11-08T13:12:28.480773381" } } \ No newline at end of file From 706fd3bd8bb6d921c981d2c6701bfa3365613f85 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Fri, 8 Nov 2024 13:23:04 +0000 Subject: [PATCH 14/41] Revert "fix ci not triggered on expected events" This reverts commit 2dfb48c258a35694590496d13d7e8f945579017f. --- .github/workflows/ci.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index e927f7b1..9c2b982e 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,12 +1,12 @@ name: nf-core CI # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors on: - push: - branches: - - dev pull_request: + branches: + - dev + - master release: - types: [published] + types: [published] workflow_dispatch: env: From 787aed1f631dff2af052b7a18b969a24690423ab Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Fri, 8 Nov 2024 13:36:14 +0000 Subject: [PATCH 15/41] add test on push --- .github/workflows/ci.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 9c2b982e..6c679615 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,6 +1,9 @@ name: nf-core CI # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors on: + push: + branches: + - dev pull_request: branches: - dev From 17ee8b69e7fc519e0cab6a69ac217de97070d65a Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Fri, 8 Nov 2024 13:46:10 +0000 Subject: [PATCH 16/41] remove all data.rds --- tests/.nftignore | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/.nftignore b/tests/.nftignore index a1c812b0..b267b09f 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -10,4 +10,4 @@ report/gsea/**/phenotype_uninvolved_lesional.*.gsea_report_for_*.tsv report/*.html report/*.zip *html -shinyngs_app/SRP254919/data.rds +shinyngs_app/**/data.rds From 9f65e57beca172623ef4424cf52a9c248ca6c943 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Fri, 8 Nov 2024 14:20:15 +0000 Subject: [PATCH 17/41] update tests and snaps --- tests/test.nf.test | 2 +- tests/test.nf.test.snap | 3 +-- tests/test_affy.nf.test | 2 +- tests/test_affy.nf.test.snap | 9 ++++----- tests/test_maxquant.nf.test | 2 +- tests/test_nogtf.nf.test | 2 +- tests/test_nogtf.nf.test.snap | 3 +-- tests/test_rnaseq_limma.nf.test | 2 +- tests/test_soft.nf.test | 2 +- tests/test_soft.nf.test.snap | 3 +-- 10 files changed, 13 insertions(+), 17 deletions(-) diff --git a/tests/test.nf.test b/tests/test.nf.test index 908e7aec..cbaf90eb 100644 --- a/tests/test.nf.test +++ b/tests/test.nf.test @@ -1,6 +1,6 @@ nextflow_pipeline { - name "Test Workflow main.nf - DIFFERENTIALABUNDANCE" + name "Test Workflow main.nf - DIFFERENTIALABUNDANCE (test)" script "../main.nf" profile "+test" tag "test" diff --git a/tests/test.nf.test.snap b/tests/test.nf.test.snap index 46831c42..829201f0 100644 --- a/tests/test.nf.test.snap +++ b/tests/test.nf.test.snap @@ -140,7 +140,6 @@ "treatment_mCherry_hND6_sample_number.mh.all.v2022.1.Mm.symbols.ranked_gene_list_hND6_versus_mCherry.tsv:md5,30cfd08715168536aab8a088009d3bc4", "treatment_mCherry_hND6_sample_number.mh.all.v2022.1.Mm.symbols.ranked_list_corr_2.png:md5,07e580fa86de237281de6a59b4d84716", "app.R:md5,bedcfc45b6cdcc2b8fe3627987e2b17a", - "data.rds:md5,deed018597462c275329a22aba95345f", "versions.yml:md5,892774f9d56ba10c8646736b7f777ecc", "Mus_musculus.anno.tsv:md5,c1d7f21e64bd00f845ec6545c123a1fb", "treatment_mCherry_hND6_.deseq2.results.tsv:md5,42ad391a5d3b2e4e7931af3088cc6400", @@ -155,6 +154,6 @@ "nf-test": "0.9.0", "nextflow": "24.10.0" }, - "timestamp": "2024-11-07T17:19:02.508819768" + "timestamp": "2024-11-08T14:00:03.015341477" } } \ No newline at end of file diff --git a/tests/test_affy.nf.test b/tests/test_affy.nf.test index 4f035ad0..1fd24c9e 100644 --- a/tests/test_affy.nf.test +++ b/tests/test_affy.nf.test @@ -1,6 +1,6 @@ nextflow_pipeline { - name "Test Workflow main.nf - DIFFERENTIALABUNDANCE" + name "Test Workflow main.nf - DIFFERENTIALABUNDANCE (affy)" script "../main.nf" profile "+test_affy" tag "affy" diff --git a/tests/test_affy.nf.test.snap b/tests/test_affy.nf.test.snap index c9fc3228..7d7281f3 100644 --- a/tests/test_affy.nf.test.snap +++ b/tests/test_affy.nf.test.snap @@ -61,6 +61,8 @@ "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_FATTY_ACID_METABOLISM.tsv", "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_G2M_CHECKPOINT.html", "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_G2M_CHECKPOINT.tsv", + "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_GLYCOLYSIS.html", + "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_GLYCOLYSIS.tsv", "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_IL2_STAT5_SIGNALING.html", "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_IL2_STAT5_SIGNALING.tsv", "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_IL6_JAK_STAT3_SIGNALING.html", @@ -87,8 +89,6 @@ "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_NOTCH_SIGNALING.tsv", "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_OXIDATIVE_PHOSPHORYLATION.html", "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_OXIDATIVE_PHOSPHORYLATION.tsv", - "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_P53_PATHWAY.html", - "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_P53_PATHWAY.tsv", "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_PEROXISOME.html", "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_PEROXISOME.tsv", "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_PROTEIN_SECRETION.html", @@ -167,6 +167,7 @@ "phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_ESTROGEN_RESPONSE_EARLY.tsv:md5,695b5bd61210e9fd4e76993cee00c63d", "phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_FATTY_ACID_METABOLISM.tsv:md5,cb069d05610994d1e43ea84de165bcd0", "phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_G2M_CHECKPOINT.tsv:md5,09eba22af78006f69a9d0cb1bee27331", + "phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_GLYCOLYSIS.tsv:md5,08c50f431cee394c0280f41345a07d96", "phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_IL2_STAT5_SIGNALING.tsv:md5,38824ee08434a02049cf7f57c43545d5", "phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_IL6_JAK_STAT3_SIGNALING.tsv:md5,ab80e349a52b1b17d350d488d552f2b6", "phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_INFLAMMATORY_RESPONSE.tsv:md5,99983d81cd0ee6bc9c5e078ea311147c", @@ -180,7 +181,6 @@ "phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_MYOGENESIS.tsv:md5,332f9386161436cd69d4b830e0f392d6", "phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_NOTCH_SIGNALING.tsv:md5,53bc5acac191f31dcdbfe62fcf396358", "phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_OXIDATIVE_PHOSPHORYLATION.tsv:md5,faab3d7cea1ff32b5c224587246ad34e", - "phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_P53_PATHWAY.tsv:md5,4070abb7bce1b665cae361d1fafadc4a", "phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_PEROXISOME.tsv:md5,66a120807b07d920c876b65b3925264c", "phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_PROTEIN_SECRETION.tsv:md5,d13300c61a1e99a0b05ef18fac74c42d", "phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY.tsv:md5,33429d1e3f2342c6c0e7b499035bd8da", @@ -193,7 +193,6 @@ "phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.gene_set_sizes.tsv:md5,77b53b0ca686ede9fe15ca448340f9f5", "phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.ranked_gene_list_lesional_versus_uninvolved.tsv:md5,72dfaeff534ba9a2b32f63524e835dc4", "app.R:md5,bedcfc45b6cdcc2b8fe3627987e2b17a", - "data.rds:md5,12443200d8ebe6a8e9d5409d5592dbc9", "versions.yml:md5,892774f9d56ba10c8646736b7f777ecc", "hgu133plus2.annotation.tsv:md5,f2b82ef12b2a2e8e575de06766583d96", "phenotype_uninvolved_lesional.limma.results.tsv:md5,686e871be0f1b435e161f84f6518cfc3", @@ -214,6 +213,6 @@ "nf-test": "0.9.0", "nextflow": "24.10.0" }, - "timestamp": "2024-11-07T18:45:19.680294927" + "timestamp": "2024-11-08T14:04:25.71001709" } } \ No newline at end of file diff --git a/tests/test_maxquant.nf.test b/tests/test_maxquant.nf.test index cb2c9556..86447bee 100644 --- a/tests/test_maxquant.nf.test +++ b/tests/test_maxquant.nf.test @@ -1,6 +1,6 @@ nextflow_pipeline { - name "Test Workflow main.nf - DIFFERENTIALABUNDANCE" + name "Test Workflow main.nf - DIFFERENTIALABUNDANCE (maxquant)" script "../main.nf" profile "+test_maxquant" tag "maxquant" diff --git a/tests/test_nogtf.nf.test b/tests/test_nogtf.nf.test index 6ddef9cd..ea685265 100644 --- a/tests/test_nogtf.nf.test +++ b/tests/test_nogtf.nf.test @@ -1,6 +1,6 @@ nextflow_pipeline { - name "Test Workflow main.nf - DIFFERENTIALABUNDANCE" + name "Test Workflow main.nf - DIFFERENTIALABUNDANCE (nogtf)" script "../main.nf" profile "+test_nogtf" tag "nogtf" diff --git a/tests/test_nogtf.nf.test.snap b/tests/test_nogtf.nf.test.snap index c8dfb7d9..c07ecb96 100644 --- a/tests/test_nogtf.nf.test.snap +++ b/tests/test_nogtf.nf.test.snap @@ -69,7 +69,6 @@ "treatment_mCherry_hND6_.deseq2.dispersion.png:md5,ed14d196fadbe460d560982ef1e2ac91", "treatment_mCherry_hND6_sample_number.deseq2.dispersion.png:md5,d0f07f97c7f5c660b173d85b85ed50b9", "app.R:md5,bedcfc45b6cdcc2b8fe3627987e2b17a", - "data.rds:md5,341874520c0d16c2eca5388e3585c6b2", "versions.yml:md5,892774f9d56ba10c8646736b7f777ecc", "treatment_mCherry_hND6_.deseq2.results.tsv:md5,d9e894aeb89aa5bc79bf7ce31304d7c0", "treatment_mCherry_hND6_.deseq2.results_filtered.tsv:md5,630820ec91287d8bcb2e5882431c09c3", @@ -83,6 +82,6 @@ "nf-test": "0.9.0", "nextflow": "24.10.0" }, - "timestamp": "2024-11-07T16:59:16.942778374" + "timestamp": "2024-11-08T14:08:09.370720729" } } \ No newline at end of file diff --git a/tests/test_rnaseq_limma.nf.test b/tests/test_rnaseq_limma.nf.test index 09b4b20c..276d82c4 100644 --- a/tests/test_rnaseq_limma.nf.test +++ b/tests/test_rnaseq_limma.nf.test @@ -1,6 +1,6 @@ nextflow_pipeline { - name "Test Workflow main.nf - DIFFERENTIALABUNDANCE" + name "Test Workflow main.nf - DIFFERENTIALABUNDANCE (limma)" script "../main.nf" profile "+test_rnaseq_limma" tag "rnaseq_limma" diff --git a/tests/test_soft.nf.test b/tests/test_soft.nf.test index 5c09e648..92ed8af5 100644 --- a/tests/test_soft.nf.test +++ b/tests/test_soft.nf.test @@ -1,6 +1,6 @@ nextflow_pipeline { - name "Test Workflow main.nf - DIFFERENTIALABUNDANCE" + name "Test Workflow main.nf - DIFFERENTIALABUNDANCE (soft)" script "../main.nf" profile "+test_soft" tag "soft" diff --git a/tests/test_soft.nf.test.snap b/tests/test_soft.nf.test.snap index dd65cd41..f4db77b6 100644 --- a/tests/test_soft.nf.test.snap +++ b/tests/test_soft.nf.test.snap @@ -59,7 +59,6 @@ "versions.yml:md5,9c47cbf6f2f30c711eb57fff84ea3736", "phenotype_uninvolved_lesional.limma.mean_difference.png:md5,570bc62fbad15b7b25eaea786a416ace", "app.R:md5,bedcfc45b6cdcc2b8fe3627987e2b17a", - "data.rds:md5,71508ad31e0fb1b69ed569c85470f660", "versions.yml:md5,892774f9d56ba10c8646736b7f777ecc", "normalised.annotation.tsv:md5,40300ae222ae35fa54daf10a1b86e830", "phenotype_uninvolved_lesional.limma.results.tsv:md5,2cfa653fffb034be4b82abf306c87bc5", @@ -71,6 +70,6 @@ "nf-test": "0.9.0", "nextflow": "24.10.0" }, - "timestamp": "2024-11-07T16:45:37.804157158" + "timestamp": "2024-11-08T14:12:26.809162392" } } \ No newline at end of file From c733ba02877d03f6efc4b6c38e1063b74ef65443 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Fri, 8 Nov 2024 15:31:31 +0000 Subject: [PATCH 18/41] add more unstable files --- tests/.nftignore | 4 ++++ tests/test_affy.nf.test | 7 ++++++- tests/test_affy.nf.test.snap | 5 +---- 3 files changed, 11 insertions(+), 5 deletions(-) diff --git a/tests/.nftignore b/tests/.nftignore index b267b09f..21b57c58 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -11,3 +11,7 @@ report/*.html report/*.zip *html shinyngs_app/**/data.rds +report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_GLYCOLYSIS.html +report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_GLYCOLYSIS.tsv +report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_P53_PATHWAY.html +report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_P53_PATHWAY.tsv diff --git a/tests/test_affy.nf.test b/tests/test_affy.nf.test index 1fd24c9e..9e8ac746 100644 --- a/tests/test_affy.nf.test +++ b/tests/test_affy.nf.test @@ -16,7 +16,12 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}', 'report/gsea/phenotype_uninvolved_lesional/**/*.png']) + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}', + 'report/gsea/phenotype_uninvolved_lesional/**/*.png', + 'report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_GLYCOLYSIS.html', + 'report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_GLYCOLYSIS.tsv', + 'report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_P53_PATHWAY.html', + 'report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_P53_PATHWAY.tsv']) // stable_path: All files in ${params.outdir}/ with stable content def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( diff --git a/tests/test_affy.nf.test.snap b/tests/test_affy.nf.test.snap index 7d7281f3..bfe2c0fc 100644 --- a/tests/test_affy.nf.test.snap +++ b/tests/test_affy.nf.test.snap @@ -61,8 +61,6 @@ "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_FATTY_ACID_METABOLISM.tsv", "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_G2M_CHECKPOINT.html", "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_G2M_CHECKPOINT.tsv", - "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_GLYCOLYSIS.html", - "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_GLYCOLYSIS.tsv", "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_IL2_STAT5_SIGNALING.html", "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_IL2_STAT5_SIGNALING.tsv", "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_IL6_JAK_STAT3_SIGNALING.html", @@ -167,7 +165,6 @@ "phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_ESTROGEN_RESPONSE_EARLY.tsv:md5,695b5bd61210e9fd4e76993cee00c63d", "phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_FATTY_ACID_METABOLISM.tsv:md5,cb069d05610994d1e43ea84de165bcd0", "phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_G2M_CHECKPOINT.tsv:md5,09eba22af78006f69a9d0cb1bee27331", - "phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_GLYCOLYSIS.tsv:md5,08c50f431cee394c0280f41345a07d96", "phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_IL2_STAT5_SIGNALING.tsv:md5,38824ee08434a02049cf7f57c43545d5", "phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_IL6_JAK_STAT3_SIGNALING.tsv:md5,ab80e349a52b1b17d350d488d552f2b6", "phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_INFLAMMATORY_RESPONSE.tsv:md5,99983d81cd0ee6bc9c5e078ea311147c", @@ -213,6 +210,6 @@ "nf-test": "0.9.0", "nextflow": "24.10.0" }, - "timestamp": "2024-11-08T14:04:25.71001709" + "timestamp": "2024-11-08T15:05:24.153458864" } } \ No newline at end of file From 2c9a55dfdb8c3efc635aa3e31d4cdbd4cde9ec3b Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Fri, 8 Nov 2024 17:16:06 +0000 Subject: [PATCH 19/41] remove sharding strategy --- .github/workflows/ci.yml | 34 ++++++++++++++++++++-------------- 1 file changed, 20 insertions(+), 14 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 6c679615..f95ad981 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -27,7 +27,7 @@ concurrency: jobs: test: - name: "${{ matrix.NXF_VER }} | ${{ matrix.profile }} | ${{ matrix.shard }}/6" + name: "${{ matrix.NXF_VER }} | ${{ matrix.test_profile }} | ${{ matrix.compute_profile }}" # Only run on push if this is the nf-core dev branch (merged PRs) if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/differentialabundance') }}" runs-on: ubuntu-latest @@ -37,7 +37,14 @@ jobs: NXF_VER: - "24.04.2" - "latest-everything" - profile: + test_profile: + - "test" + - "nogtf" + - "affy" + - "maxquant" + - "soft" + - "rnaseq_limma" + compute_profile: - "docker" - "singularity" isMaster: @@ -45,10 +52,9 @@ jobs: # Exclude conda and singularity on dev exclude: - isMaster: false - profile: "conda" + compute_profile: "conda" - isMaster: false - profile: "singularity" - shard: [1, 2, 3, 4, 5, 6] + compute_profile: "singularity" steps: - name: Check out pipeline code uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 @@ -61,17 +67,17 @@ jobs: version: "${{ matrix.NXF_VER }}" - name: Set up Apptainer - if: matrix.profile == 'singularity' + if: matrix.compute_profile == 'singularity' uses: eWaterCycle/setup-apptainer@main - name: Set up Singularity - if: matrix.profile == 'singularity' + if: matrix.compute_profile == 'singularity' run: | mkdir -p $NXF_SINGULARITY_CACHEDIR mkdir -p $NXF_SINGULARITY_LIBRARYDIR - name: Set up Miniconda - if: matrix.profile == 'conda' + if: matrix.compute_profile == 'conda' uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 with: miniconda-version: "latest" @@ -80,7 +86,7 @@ jobs: channels: conda-forge,bioconda - name: Set up Conda - if: matrix.profile == 'conda' + if: matrix.compute_profile == 'conda' run: | echo $(realpath $CONDA)/condabin >> $GITHUB_PATH echo $(realpath python) >> $GITHUB_PATH @@ -102,15 +108,15 @@ jobs: with: version: ${{ env.NFT_VER }} - - name: Run Tests (Shard ${{ matrix.shard }}/6) + - name: Run Tests (${{matrix.NXF_VER}} | ${{matrix.test_profile}} | ${{matrix.compute_profile}}) run: | nf-test test \ --ci \ - --shard ${{ matrix.shard }}/6 \ + --tag ${{matrix.test_profile}} \ --changed-since HEAD^ \ - --profile "+${{ matrix.profile }}" \ - --filter pipeline \ - --junitxml=test.xml + --profile "+${{ matrix.compute_profile }}" \ + --junitxml=test.xml \ + --debug - name: Publish Test Report uses: mikepenz/action-junit-report@v3 From 6cc4effcdc1de8474c58e9b2a779b35db0ec5232 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Mon, 11 Nov 2024 12:28:37 +0000 Subject: [PATCH 20/41] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 15f6c833..8fd83c9e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added +- [[#343](https://github.com/nf-core/differentialabundance/pull/343)] - Add pipeline-level nf-tests ([@atrigila](https://github.com/atrigila), review by [@pinin4fjords](https://github.com/pinin4fjords)) and [@nschcolnicov](https://github.com/nschcolnicov) - [[#286](https://github.com/nf-core/differentialabundance/pull/286)] - Integration of limma voom for rnaseq data ([@KamilMaliszArdigen](https://github.com/KamilMaliszArdigen), review by [@pinin4fjords](https://github.com/pinin4fjords)) ### Fixed From ce524cef8fe5d048f6fcbdd292203bffb3b9c569 Mon Sep 17 00:00:00 2001 From: Anabella Trigila <18577080+atrigila@users.noreply.github.com> Date: Mon, 11 Nov 2024 11:10:08 -0300 Subject: [PATCH 21/41] Update CHANGELOG.md Co-authored-by: Jonathan Manning --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8fd83c9e..708f4c3d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,7 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added -- [[#343](https://github.com/nf-core/differentialabundance/pull/343)] - Add pipeline-level nf-tests ([@atrigila](https://github.com/atrigila), review by [@pinin4fjords](https://github.com/pinin4fjords)) and [@nschcolnicov](https://github.com/nschcolnicov) +- [[#343](https://github.com/nf-core/differentialabundance/pull/343)] - Add pipeline-level nf-tests ([@atrigila](https://github.com/atrigila), review by [@pinin4fjords](https://github.com/pinin4fjords)) and [@nschcolnicov](https://github.com/nschcolnicov)) - [[#286](https://github.com/nf-core/differentialabundance/pull/286)] - Integration of limma voom for rnaseq data ([@KamilMaliszArdigen](https://github.com/KamilMaliszArdigen), review by [@pinin4fjords](https://github.com/pinin4fjords)) ### Fixed From f1123dc562e0e185e7c828d19931211ebf01154c Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Mon, 11 Nov 2024 14:14:44 +0000 Subject: [PATCH 22/41] use regex in replacement --- workflows/differentialabundance.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/differentialabundance.nf b/workflows/differentialabundance.nf index d97e7153..e49bebda 100644 --- a/workflows/differentialabundance.nf +++ b/workflows/differentialabundance.nf @@ -322,7 +322,7 @@ workflow DIFFERENTIALABUNDANCE { .map{it[1]} .splitCsv ( header:true, sep:'\t' ) .map{ - it.blocking = it.blocking.replace('NA', '') + it.blocking = it.blocking.replaceAll('^NA$', '') if (!it.id){ it.id = it.values().join('_') } From ca66b2cf721ae64982c32bb387c8aeee0b928292 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Mon, 11 Nov 2024 17:09:11 +0000 Subject: [PATCH 23/41] add changelog template --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index e9503bf1..1db9efaf 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Fixed +- [[#344](https://github.com/nf-core/differentialabundance/pull/344)] - Fixed replacement of NA sub-strings + ([@atrigila](https://github.com/atrigila), suggested by [@BEFH](https://github.com/BEFH), review by [@](https://github.com/)) - [[#342](https://github.com/nf-core/differentialabundance/pull/342)] - Fixed incorrectly colored dots in report volcano plots for logFC thresholds <1 ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords)) - [[#330](https://github.com/nf-core/differentialabundance/pull/330)] - Fixed broken docs by removing g:profiler colons ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords)) - [[#304](https://github.com/nf-core/differentialabundance/pull/304)] - Removed TXT file options from nextflow_schema where they are equivalent to TSV to make the input files clearer ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords)) From 88e94013a80b01f9ce1ea98012e968dc078029fb Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Tue, 12 Nov 2024 00:17:46 +0000 Subject: [PATCH 24/41] update changelog --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1db9efaf..6f9c850c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,13 +7,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added -- [[#343](https://github.com/nf-core/differentialabundance/pull/343)] - Add pipeline-level nf-tests ([@atrigila](https://github.com/atrigila), review by [@pinin4fjords](https://github.com/pinin4fjords)) and [@nschcolnicov](https://github.com/nschcolnicov)) +- [[#343](https://github.com/nf-core/differentialabundance/pull/343)] - Add pipeline-level nf-tests ([@atrigila](https://github.com/atrigila), review by [@pinin4fjords](https://github.com/pinin4fjords) and [@nschcolnicov](https://github.com/nschcolnicov)) - [[#286](https://github.com/nf-core/differentialabundance/pull/286)] - Integration of limma voom for rnaseq data ([@KamilMaliszArdigen](https://github.com/KamilMaliszArdigen), review by [@pinin4fjords](https://github.com/pinin4fjords)) ### Fixed - [[#344](https://github.com/nf-core/differentialabundance/pull/344)] - Fixed replacement of NA sub-strings - ([@atrigila](https://github.com/atrigila), suggested by [@BEFH](https://github.com/BEFH), review by [@](https://github.com/)) + ([@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)) - [[#342](https://github.com/nf-core/differentialabundance/pull/342)] - Fixed incorrectly colored dots in report volcano plots for logFC thresholds <1 ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords)) - [[#330](https://github.com/nf-core/differentialabundance/pull/330)] - Fixed broken docs by removing g:profiler colons ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords)) - [[#304](https://github.com/nf-core/differentialabundance/pull/304)] - Removed TXT file options from nextflow_schema where they are equivalent to TSV to make the input files clearer ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords)) From 25691799fe4c5dc6b02cddb04bc36f95ff0ef353 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Wed, 13 Nov 2024 13:18:52 +0000 Subject: [PATCH 25/41] add plot by biotype --- CHANGELOG.md | 1 + assets/differentialabundance_report.Rmd | 19 +++++++++++++++++++ 2 files changed, 20 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6f9c850c..4805ecb0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added +- [[#345](https://github.com/nf-core/differentialabundance/pull/345)] - Plot differentially expressed genes by gene biotype ([@atrigila](https://github.com/atrigila), review by [@](https://github.com/)) - [[#343](https://github.com/nf-core/differentialabundance/pull/343)] - Add pipeline-level nf-tests ([@atrigila](https://github.com/atrigila), review by [@pinin4fjords](https://github.com/pinin4fjords) and [@nschcolnicov](https://github.com/nschcolnicov)) - [[#286](https://github.com/nf-core/differentialabundance/pull/286)] - Integration of limma voom for rnaseq data ([@KamilMaliszArdigen](https://github.com/KamilMaliszArdigen), review by [@pinin4fjords](https://github.com/pinin4fjords)) diff --git a/assets/differentialabundance_report.Rmd b/assets/differentialabundance_report.Rmd index ce6bb812..503c5798 100644 --- a/assets/differentialabundance_report.Rmd +++ b/assets/differentialabundance_report.Rmd @@ -895,6 +895,25 @@ for (i in 1:nrow(contrasts)){ if (nrow(contrast_de) > 0){ contrast_de <- round_dataframe_columns(contrast_de, digits=params$report_round_digits) print( htmltools::tagList(datatable(contrast_de, caption = paste('Differential genes', dir, 'in', contrast_descriptions[i], " (check", differential_files[[i]], "for more detail)"), rownames = FALSE) )) + + # Plot Differentially Expressed Genes by Gene Biotype + gene_biotype_table <- contrast_de %>% + group_by(`Gene biotype`) %>% + dplyr::summarise(count = dplyr::n(), .groups = 'drop') %>% + dplyr::filter(count > 0) %>% + dplyr::arrange(desc(count)) + + gene_biotype_plot <- ggplot(gene_biotype_table, aes(x = reorder(`Gene biotype`, -count), y = count)) + + geom_bar(stat = "identity", position = position_dodge()) + + labs( + title = paste0("Differentially Expressed Genes by Gene Biotype (", dir, ")"), + x = "Gene Biotype", + y = "Number of Differentially Expressed Genes" ) + + theme_minimal() + + theme(axis.text.x = element_text(angle = 45, hjust = 1)) + + print(gene_biotype_plot) + }else{ cat(paste0("No significantly differential '", dir, "' genes.\n\n")) } From 53a86295b398aff5d5c66110073d636ff2bbb90d Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Wed, 13 Nov 2024 15:07:01 +0000 Subject: [PATCH 26/41] remove unnecesary dplyr --- assets/differentialabundance_report.Rmd | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/assets/differentialabundance_report.Rmd b/assets/differentialabundance_report.Rmd index 503c5798..240c3ffe 100644 --- a/assets/differentialabundance_report.Rmd +++ b/assets/differentialabundance_report.Rmd @@ -899,9 +899,9 @@ for (i in 1:nrow(contrasts)){ # Plot Differentially Expressed Genes by Gene Biotype gene_biotype_table <- contrast_de %>% group_by(`Gene biotype`) %>% - dplyr::summarise(count = dplyr::n(), .groups = 'drop') %>% - dplyr::filter(count > 0) %>% - dplyr::arrange(desc(count)) + summarise(count = dplyr::n(), .groups = 'drop') %>% + filter(count > 0) %>% + arrange(desc(count)) gene_biotype_plot <- ggplot(gene_biotype_table, aes(x = reorder(`Gene biotype`, -count), y = count)) + geom_bar(stat = "identity", position = position_dodge()) + From 8e6f078a84b2873d663762cc1bec8cc92c888900 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Wed, 13 Nov 2024 15:12:47 +0000 Subject: [PATCH 27/41] update changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4805ecb0..da3c061f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,7 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added -- [[#345](https://github.com/nf-core/differentialabundance/pull/345)] - Plot differentially expressed genes by gene biotype ([@atrigila](https://github.com/atrigila), review by [@](https://github.com/)) +- [[#345](https://github.com/nf-core/differentialabundance/pull/345)] - Plot differentially expressed genes by gene biotype ([@atrigila](https://github.com/atrigila), review by [@grst](https://github.com/grst)) - [[#343](https://github.com/nf-core/differentialabundance/pull/343)] - Add pipeline-level nf-tests ([@atrigila](https://github.com/atrigila), review by [@pinin4fjords](https://github.com/pinin4fjords) and [@nschcolnicov](https://github.com/nschcolnicov)) - [[#286](https://github.com/nf-core/differentialabundance/pull/286)] - Integration of limma voom for rnaseq data ([@KamilMaliszArdigen](https://github.com/KamilMaliszArdigen), review by [@pinin4fjords](https://github.com/pinin4fjords)) From 3b48cf3a5064e014469f855f683b5bd57a2e8e10 Mon Sep 17 00:00:00 2001 From: nschcolnicov Date: Wed, 13 Nov 2024 15:21:49 +0000 Subject: [PATCH 28/41] Update test full profile --- CHANGELOG.md | 2 ++ conf/test_full.config | 2 +- nextflow.config | 22 +++++++++++----------- 3 files changed, 14 insertions(+), 12 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6f9c850c..e9aca2ff 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -26,6 +26,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Changed +- [[#347](https://github.com/nf-core/differentialabundance/pull/272)] - Update test_full profile matrix file and indentation of profiles in nextflow.config [@nschcolnicov](https://github.com/nschcolnicov) + ## v1.5.0 - 2024-05-08 ### `Added` diff --git a/conf/test_full.config b/conf/test_full.config index dcc87126..1ae41281 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -17,7 +17,7 @@ params { // Input data input = 'https://raw.githubusercontent.com/nf-core/test-datasets/differentialabundance/testdata/rnaseq_featurecounts_sample_preparations.tsv' contrasts = 'https://raw.githubusercontent.com/nf-core/test-datasets/differentialabundance/testdata/rnaseq_featurecounts_contrast_file.csv' - matrix = 'https://raw.githubusercontent.com/nf-core/test-datasets/differentialabundance/testdata/rnaseq_featurecounts_merged_gene_counts.txt' + matrix = 'https://raw.githubusercontent.com/nf-core/test-datasets/differentialabundance/testdata/rnaseq_featurecounts_merged_gene_counts.tsv' gtf = 'https://ftp.ensembl.org/pub/release-81/gtf/mus_musculus/Mus_musculus.GRCm38.81.gtf.gz' // Configure inputs diff --git a/nextflow.config b/nextflow.config index a22e6736..230100ac 100644 --- a/nextflow.config +++ b/nextflow.config @@ -324,18 +324,18 @@ profiles { executor.cpus = 4 executor.memory = 8.GB } - test { includeConfig 'conf/test.config' } - test_nogtf { includeConfig 'conf/test_nogtf.config' } - test_full { includeConfig 'conf/test_full.config' } - affy { includeConfig 'conf/affy.config' } - maxquant { includeConfig 'conf/maxquant.config' } - rnaseq { includeConfig 'conf/rnaseq.config' } - rnaseq_limma { includeConfig 'conf/rnaseq_limma.config' } + test { includeConfig 'conf/test.config' } + test_nogtf { includeConfig 'conf/test_nogtf.config' } + test_full { includeConfig 'conf/test_full.config' } + affy { includeConfig 'conf/affy.config' } + maxquant { includeConfig 'conf/maxquant.config' } + rnaseq { includeConfig 'conf/rnaseq.config' } + rnaseq_limma { includeConfig 'conf/rnaseq_limma.config' } test_rnaseq_limma { includeConfig 'conf/test_rnaseq_limma.config' } - soft {includeConfig 'conf/soft.config'} - test_affy { includeConfig 'conf/test_affy.config' } - test_maxquant { includeConfig 'conf/test_maxquant.config' } - test_soft {includeConfig 'conf/test_soft.config' } + soft { includeConfig 'conf/soft.config' } + test_affy { includeConfig 'conf/test_affy.config' } + test_maxquant { includeConfig 'conf/test_maxquant.config' } + test_soft { includeConfig 'conf/test_soft.config' } } // Load nf-core custom profiles from different Institutions From 55eb8a069934f30ff2995b437a3e11935beda5f8 Mon Sep 17 00:00:00 2001 From: nschcolnicov Date: Wed, 13 Nov 2024 15:49:01 +0000 Subject: [PATCH 29/41] Update CHANGELOG --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e9aca2ff..e7b79a3e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -26,7 +26,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Changed -- [[#347](https://github.com/nf-core/differentialabundance/pull/272)] - Update test_full profile matrix file and indentation of profiles in nextflow.config [@nschcolnicov](https://github.com/nschcolnicov) +- [[#348](https://github.com/nf-core/differentialabundance/pull/348)] - Update test_full profile matrix file and indentation of profiles in nextflow.config ([@nschcolnicov](https://github.com/nschcolnicov), review by [@WackerO](https://github.com/WackerO) and [@pinin4fjords](https://github.com/pinin4fjords)) ## v1.5.0 - 2024-05-08 From 9caa45b8476b0fa87d4e53fe801bb4cd097cc477 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alan=20M=C3=B6bbs?= Date: Thu, 14 Nov 2024 13:48:50 +0000 Subject: [PATCH 30/41] compare rows before and after merging and print the warnings if necessary --- assets/differentialabundance_report.Rmd | 58 ++++++++++++++++++++----- 1 file changed, 47 insertions(+), 11 deletions(-) diff --git a/assets/differentialabundance_report.Rmd b/assets/differentialabundance_report.Rmd index 240c3ffe..ab176d4c 100644 --- a/assets/differentialabundance_report.Rmd +++ b/assets/differentialabundance_report.Rmd @@ -370,10 +370,17 @@ differential_files <- lapply(contrasts$id, function(d){ file.path(params$input_dir, paste0(gsub(' |;', '_', d), differential_file_suffix)) }) -differential_results <- lapply(differential_files, function(diff_file){ - if (! file.exists(diff_file)){ +# Initialize vector to store warning messages before merging tables +warnings_list <- c() + +# Read differential results and merge with features table +results <- lapply(differential_files, function(diff_file) { + warnings <- c() # Initialize local warning vector + + if (!file.exists(diff_file)) { stop(paste("Differential file", diff_file, "does not exist")) } + diff <- read_differential( diff_file, feature_id_column = params$differential_feature_id_column, @@ -382,19 +389,43 @@ differential_results <- lapply(differential_files, function(diff_file){ qval_column = params$differential_qval_column ) - # If fold changes are not logged already, log them (we assume they're logged - # later on) - - if (! params$differential_foldchanges_logged){ + # If fold changes are not logged already, log them + if (!params$differential_foldchanges_logged) { diff[[params$differential_fc_column]] <- log2(diff[[params$differential_fc_column]]) } # Annotate differential tables if possible - if (! is.null(params$features)){ - diff <- merge(features, diff, by.x = params$features_id_col, by.y = params$differential_feature_id_column) + if (!is.null(params$features)) { + + # Merge tables + diff_features <- merge(features, diff, by.x = params$features_id_col, by.y = params$differential_feature_id_column) + + # Get number of rows before and after merging + length_diff <- as.numeric(nrow(diff)) + length_features <- as.numeric(nrow(diff_features)) + + # Compare numbers and report + if (length_diff != length_features) { + warnings <- c(warnings, + paste0( + '

WARNING: Some rows from the differential expressed table (', basename(diff_file), ') were lost after merging with features table (', basename(params$features), ').\n', + 'Rows in diff table: ', length_diff, '.\n', + 'Rows in merged table: ', length_features, '.

\n' + ) + ) + } + } else { + diff_features <- diff } - diff + + # Return both the results and the local warnings + list(diff_features = diff_features, warnings = warnings) }) + +# Separate differential_results and warnings_list from results +differential_results <- lapply(results, `[[`, "diff_features") +warnings_list <- unlist(lapply(results, `[[`, "warnings")) + names(differential_results) <- contrasts$id ``` @@ -787,7 +818,6 @@ foo <- lapply(names(p_value_types), function(pvt){ ``` ```{r, echo=FALSE, results='asis', eval = FALSE} - differential_summary_string <- paste( paste( lapply( @@ -806,7 +836,13 @@ cat(differential_summary_string) ### Differential `r params$features_type` details -```{r, echo=FALSE, results='asis'} +```{r, echo=FALSE, results='asis', warning=FALSE, message=FALSE} + +# Display all warnings related to number of rows +if (length(warnings_list) > 0) { + for (warning in warnings_list) { cat(warning) } +} + for (i in 1:nrow(contrasts)){ cat("\n#### ", contrast_descriptions[i], " {.tabset}\n") From c7205bf664781b258a9c84c49555e15adc701c70 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alan=20M=C3=B6bbs?= Date: Thu, 14 Nov 2024 14:29:19 +0000 Subject: [PATCH 31/41] change color --- assets/differentialabundance_report.Rmd | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/assets/differentialabundance_report.Rmd b/assets/differentialabundance_report.Rmd index ab176d4c..b8011c26 100644 --- a/assets/differentialabundance_report.Rmd +++ b/assets/differentialabundance_report.Rmd @@ -399,6 +399,8 @@ results <- lapply(differential_files, function(diff_file) { # Merge tables diff_features <- merge(features, diff, by.x = params$features_id_col, by.y = params$differential_feature_id_column) + # test + diff_features <- diff_features[1:50,] # Get number of rows before and after merging length_diff <- as.numeric(nrow(diff)) @@ -408,7 +410,7 @@ results <- lapply(differential_files, function(diff_file) { if (length_diff != length_features) { warnings <- c(warnings, paste0( - '

WARNING: Some rows from the differential expressed table (', basename(diff_file), ') were lost after merging with features table (', basename(params$features), ').\n', + '

WARNING: Some rows from the differential expressed table (', basename(diff_file), ') were lost after merging with features table (', basename(params$features), ').\n', 'Rows in diff table: ', length_diff, '.\n', 'Rows in merged table: ', length_features, '.

\n' ) From 993d74f3b2bdf638ee5e2f90cdb7d39455d46604 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alan=20M=C3=B6bbs?= Date: Thu, 14 Nov 2024 15:08:50 +0000 Subject: [PATCH 32/41] Update changelog and remove test lines --- CHANGELOG.md | 1 + assets/differentialabundance_report.Rmd | 2 -- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6bbc2f5c..1ca662c3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [[#345](https://github.com/nf-core/differentialabundance/pull/345)] - Plot differentially expressed genes by gene biotype ([@atrigila](https://github.com/atrigila), review by [@grst](https://github.com/grst)) - [[#343](https://github.com/nf-core/differentialabundance/pull/343)] - Add pipeline-level nf-tests ([@atrigila](https://github.com/atrigila), review by [@pinin4fjords](https://github.com/pinin4fjords) and [@nschcolnicov](https://github.com/nschcolnicov)) - [[#286](https://github.com/nf-core/differentialabundance/pull/286)] - Integration of limma voom for rnaseq data ([@KamilMaliszArdigen](https://github.com/KamilMaliszArdigen), review by [@pinin4fjords](https://github.com/pinin4fjords)) +- [[#354](https://github.com/nf-core/differentialabundance/pull/354)] - Warning message within the R Markdown report to control when genes don't have annotation data ([@alanmmobbs93](https://github.com/alanmmobbs93)). Review by [@WackerO](https://github.com/WackerO) and [@pinin4fjords](https://github.com/pinin4fjords). ### Fixed diff --git a/assets/differentialabundance_report.Rmd b/assets/differentialabundance_report.Rmd index b8011c26..d2be3b2f 100644 --- a/assets/differentialabundance_report.Rmd +++ b/assets/differentialabundance_report.Rmd @@ -399,8 +399,6 @@ results <- lapply(differential_files, function(diff_file) { # Merge tables diff_features <- merge(features, diff, by.x = params$features_id_col, by.y = params$differential_feature_id_column) - # test - diff_features <- diff_features[1:50,] # Get number of rows before and after merging length_diff <- as.numeric(nrow(diff)) From 4382441f013904143966f25cdef54dba1a9492ec Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alan=20M=C3=B6bbs?= <64787947+alanmmobbs93@users.noreply.github.com> Date: Fri, 15 Nov 2024 12:14:37 -0300 Subject: [PATCH 33/41] Update assets/differentialabundance_report.Rmd Co-authored-by: Jonathan Manning --- assets/differentialabundance_report.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/assets/differentialabundance_report.Rmd b/assets/differentialabundance_report.Rmd index d2be3b2f..f6c2143f 100644 --- a/assets/differentialabundance_report.Rmd +++ b/assets/differentialabundance_report.Rmd @@ -408,7 +408,7 @@ results <- lapply(differential_files, function(diff_file) { if (length_diff != length_features) { warnings <- c(warnings, paste0( - '

WARNING: Some rows from the differential expressed table (', basename(diff_file), ') were lost after merging with features table (', basename(params$features), ').\n', + '

WARNING: Some rows from the differential expressed table (', basename(diff_file), ') were absent from the features table (', basename(params$features), ') and lost on merge.\n', 'Rows in diff table: ', length_diff, '.\n', 'Rows in merged table: ', length_features, '.

\n' ) From e7a54f45ca7e5cb182fc592ca3075c07e77a9638 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alan=20M=C3=B6bbs?= Date: Fri, 15 Nov 2024 18:18:01 +0000 Subject: [PATCH 34/41] differentiate between more or less rows and report IDs --- assets/differentialabundance_report.Rmd | 38 +++++++++++++++++++++---- 1 file changed, 33 insertions(+), 5 deletions(-) diff --git a/assets/differentialabundance_report.Rmd b/assets/differentialabundance_report.Rmd index f6c2143f..e3eb0256 100644 --- a/assets/differentialabundance_report.Rmd +++ b/assets/differentialabundance_report.Rmd @@ -401,19 +401,47 @@ results <- lapply(differential_files, function(diff_file) { diff_features <- merge(features, diff, by.x = params$features_id_col, by.y = params$differential_feature_id_column) # Get number of rows before and after merging - length_diff <- as.numeric(nrow(diff)) - length_features <- as.numeric(nrow(diff_features)) + rows_diff <- as.numeric(nrow(diff)) + rows_diff_features <- as.numeric(nrow(diff_features)) + + # Check that all IDs were conserved + conserved_ids <- all( diff[[params$differential_feature_id_column]] %in% diff_features[[params$features_id_col]] ) + + ## Check if all IDs are present + if (!conserved_ids) { + missing_ids <- setdiff(diff[[params$differential_feature_id_column]], diff_features[[params$features_id_col]]) + warnings <- c(warnings, + paste0( + '

WARNING:', length(missing_ids),' IDs from the differential expressed table (', basename(diff_file), ') were absent from the features table (', basename(params$features), ') and lost on merge.\n', + 'Missing IDs in diff table: ', paste(missing_ids, collapse = ' '), '.\n', + 'Rows in merged table: ', rows_diff_features, '.

\n' + ) + ) + } # Compare numbers and report - if (length_diff != length_features) { + ## Check if features_diff has fewer rows, it would indicate lost of info + if ( rows_diff_features < rows_diff ) { warnings <- c(warnings, paste0( '

WARNING: Some rows from the differential expressed table (', basename(diff_file), ') were absent from the features table (', basename(params$features), ') and lost on merge.\n', - 'Rows in diff table: ', length_diff, '.\n', - 'Rows in merged table: ', length_features, '.

\n' + 'Rows in diff table: ', rows_diff, '.\n', + 'Rows in merged table: ', rows_diff_features, '.

\n' ) ) } + + ## Check if features_diff has more rows, it could indicate duplications + if ( rows_diff_features > rows_diff ) { + warnings <- c(warnings, + paste0( + '

WARNING: Some rows from the differential expressed table (', basename(diff_file), ') were duplicated on feature table (', basename(params$features), ').\n', + 'Rows in diff table: ', rows_diff, '.\n', + 'Rows in merged table: ', rows_diff_features, '.

\n' + ) + ) + } + } else { diff_features <- diff } From 4a3d212289dcb604925c47210520c99399dc2b66 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Sun, 17 Nov 2024 21:41:15 +0000 Subject: [PATCH 35/41] always run tests --- .github/workflows/ci.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index f95ad981..00b0a0d2 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -113,7 +113,6 @@ jobs: nf-test test \ --ci \ --tag ${{matrix.test_profile}} \ - --changed-since HEAD^ \ --profile "+${{ matrix.compute_profile }}" \ --junitxml=test.xml \ --debug From 44a73308223791f04f3b23fd62331286e010f79d Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Sun, 17 Nov 2024 21:41:29 +0000 Subject: [PATCH 36/41] check if column exists --- assets/differentialabundance_report.Rmd | 40 ++++++++++++++----------- 1 file changed, 22 insertions(+), 18 deletions(-) diff --git a/assets/differentialabundance_report.Rmd b/assets/differentialabundance_report.Rmd index 240c3ffe..5e92e3c0 100644 --- a/assets/differentialabundance_report.Rmd +++ b/assets/differentialabundance_report.Rmd @@ -896,24 +896,28 @@ for (i in 1:nrow(contrasts)){ contrast_de <- round_dataframe_columns(contrast_de, digits=params$report_round_digits) print( htmltools::tagList(datatable(contrast_de, caption = paste('Differential genes', dir, 'in', contrast_descriptions[i], " (check", differential_files[[i]], "for more detail)"), rownames = FALSE) )) - # Plot Differentially Expressed Genes by Gene Biotype - gene_biotype_table <- contrast_de %>% - group_by(`Gene biotype`) %>% - summarise(count = dplyr::n(), .groups = 'drop') %>% - filter(count > 0) %>% - arrange(desc(count)) - - gene_biotype_plot <- ggplot(gene_biotype_table, aes(x = reorder(`Gene biotype`, -count), y = count)) + - geom_bar(stat = "identity", position = position_dodge()) + - labs( - title = paste0("Differentially Expressed Genes by Gene Biotype (", dir, ")"), - x = "Gene Biotype", - y = "Number of Differentially Expressed Genes" ) + - theme_minimal() + - theme(axis.text.x = element_text(angle = 45, hjust = 1)) - - print(gene_biotype_plot) - + # Check if Gene biotype column exists + if ("Gene biotype" %in% colnames(contrast_de)) { + # Plot Differentially Expressed Genes by Gene Biotype + gene_biotype_table <- contrast_de %>% + group_by(`Gene biotype`) %>% + summarise(count = dplyr::n(), .groups = 'drop') %>% + filter(count > 0) %>% + arrange(desc(count)) + + gene_biotype_plot <- ggplot(gene_biotype_table, aes(x = reorder(`Gene biotype`, -count), y = count)) + + geom_bar(stat = "identity", position = position_dodge()) + + labs( + title = paste0("Differentially Expressed Genes by Gene Biotype (", dir, ")"), + x = "Gene Biotype", + y = "Number of Differentially Expressed Genes" ) + + theme_minimal() + + theme(axis.text.x = element_text(angle = 45, hjust = 1)) + + print(gene_biotype_plot) + } else { + cat("Column 'Gene biotype' does not exist. Skipping plot.\n") + } }else{ cat(paste0("No significantly differential '", dir, "' genes.\n\n")) } From f59c538f508ef64586b1c7592e72bfb7be0ea9de Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Sun, 17 Nov 2024 21:41:49 +0000 Subject: [PATCH 37/41] update tests with versions --- tests/.nftignore | 6 ++--- tests/test.nf.test | 2 ++ tests/test.nf.test.snap | 34 +++++++++++++++++++++++++++- tests/test_affy.nf.test | 8 +++---- tests/test_affy.nf.test.snap | 32 +++++++++++++++++++++++++- tests/test_maxquant.nf.test | 2 ++ tests/test_maxquant.nf.test.snap | 28 ++++++++++++++++++++++- tests/test_nogtf.nf.test | 2 ++ tests/test_nogtf.nf.test.snap | 22 +++++++++++++++++- tests/test_rnaseq_limma.nf.test | 2 ++ tests/test_rnaseq_limma.nf.test.snap | 34 +++++++++++++++++++++++++++- tests/test_soft.nf.test | 2 ++ tests/test_soft.nf.test.snap | 26 ++++++++++++++++++++- 13 files changed, 186 insertions(+), 14 deletions(-) diff --git a/tests/.nftignore b/tests/.nftignore index 21b57c58..cfb2b95c 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -11,7 +11,5 @@ report/*.html report/*.zip *html shinyngs_app/**/data.rds -report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_GLYCOLYSIS.html -report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_GLYCOLYSIS.tsv -report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_P53_PATHWAY.html -report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_P53_PATHWAY.tsv +report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_GLYCOLYSIS.{html,tsv} +report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_P53_PATHWAY.{html,tsv} diff --git a/tests/test.nf.test b/tests/test.nf.test index cbaf90eb..744dc9c5 100644 --- a/tests/test.nf.test +++ b/tests/test.nf.test @@ -24,6 +24,8 @@ nextflow_pipeline { { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/collated_versions.yml"), // All stable path name, with a relative path stable_name, // All files with stable contents diff --git a/tests/test.nf.test.snap b/tests/test.nf.test.snap index 829201f0..c270c2f6 100644 --- a/tests/test.nf.test.snap +++ b/tests/test.nf.test.snap @@ -2,6 +2,38 @@ "Test profile": { "content": [ 21, + { + "DESEQ2_DIFFERENTIAL": { + "r-base": "4.1.3", + "bioconductor-deseq2": "1.34.0" + }, + "GSEA_GSEA": { + "gsea": "4.3.2" + }, + "GTF_TO_TABLE": { + "atlas-gene-annotation-manipulation": "1.1.1" + }, + "GUNZIP_GTF": { + "gunzip": 1.1 + }, + "PLOT_DIFFERENTIAL": { + "r-base": "4.3.3", + "r-shinyngs": "2.0.0" + }, + "PLOT_EXPLORATORY": { + "r-shinyngs": "2.0.0" + }, + "TABULAR_TO_GSEA_CHIP": { + "bash": "4.2.25 3" + }, + "VALIDATOR": { + "r-base": "4.3.3", + "r-shinyngs": "2.0.0" + }, + "Workflow": { + "nf-core/differentialabundance": "v1.6.0dev" + } + }, [ "other", "other/deseq2", @@ -154,6 +186,6 @@ "nf-test": "0.9.0", "nextflow": "24.10.0" }, - "timestamp": "2024-11-08T14:00:03.015341477" + "timestamp": "2024-11-17T21:24:54.504828126" } } \ No newline at end of file diff --git a/tests/test_affy.nf.test b/tests/test_affy.nf.test index 9e8ac746..5fab9052 100644 --- a/tests/test_affy.nf.test +++ b/tests/test_affy.nf.test @@ -18,10 +18,8 @@ nextflow_pipeline { // stable_name: All files + folders in ${params.outdir}/ with a stable name def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}', 'report/gsea/phenotype_uninvolved_lesional/**/*.png', - 'report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_GLYCOLYSIS.html', - 'report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_GLYCOLYSIS.tsv', - 'report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_P53_PATHWAY.html', - 'report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_P53_PATHWAY.tsv']) + 'report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_GLYCOLYSIS.{html,tsv}', + 'report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_P53_PATHWAY.{html,tsv}']) // stable_path: All files in ${params.outdir}/ with stable content def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( @@ -29,6 +27,8 @@ nextflow_pipeline { { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/collated_versions.yml"), // All stable path name, with a relative path stable_name, // All files with stable contents diff --git a/tests/test_affy.nf.test.snap b/tests/test_affy.nf.test.snap index bfe2c0fc..0e0ffd60 100644 --- a/tests/test_affy.nf.test.snap +++ b/tests/test_affy.nf.test.snap @@ -2,6 +2,36 @@ "Test affy profile": { "content": [ 16, + { + "AFFY_JUSTRMA_RAW": { + "r-base": "4.3.1", + "bioconductor-affy": "1.78.0" + }, + "GSEA_GSEA": { + "gsea": "4.3.2" + }, + "LIMMA_DIFFERENTIAL": { + "r-base": "4.3.3", + "bioconductor-limma": "3.58.1" + }, + "PLOT_DIFFERENTIAL": { + "r-base": "4.3.3", + "r-shinyngs": "2.0.0" + }, + "PLOT_EXPLORATORY": { + "r-shinyngs": "2.0.0" + }, + "TABULAR_TO_GSEA_CHIP": { + "bash": "4.2.25 3" + }, + "VALIDATOR": { + "r-base": "4.3.3", + "r-shinyngs": "2.0.0" + }, + "Workflow": { + "nf-core/differentialabundance": "v1.6.0dev" + } + }, [ "other", "other/affy", @@ -210,6 +240,6 @@ "nf-test": "0.9.0", "nextflow": "24.10.0" }, - "timestamp": "2024-11-08T15:05:24.153458864" + "timestamp": "2024-11-17T21:29:47.480048632" } } \ No newline at end of file diff --git a/tests/test_maxquant.nf.test b/tests/test_maxquant.nf.test index 86447bee..a9c7cc7f 100644 --- a/tests/test_maxquant.nf.test +++ b/tests/test_maxquant.nf.test @@ -24,6 +24,8 @@ nextflow_pipeline { { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/collated_versions.yml"), // All stable path name, with a relative path stable_name, // All files with stable contents diff --git a/tests/test_maxquant.nf.test.snap b/tests/test_maxquant.nf.test.snap index 28acf7e4..3782d8e2 100644 --- a/tests/test_maxquant.nf.test.snap +++ b/tests/test_maxquant.nf.test.snap @@ -2,6 +2,32 @@ "Test maxquant profile": { "content": [ 20, + { + "LIMMA_DIFFERENTIAL": { + "r-base": "4.3.3", + "bioconductor-limma": "3.58.1" + }, + "PLOT_DIFFERENTIAL": { + "r-base": "4.3.3", + "r-shinyngs": "2.0.0" + }, + "PLOT_EXPLORATORY": { + "r-shinyngs": "2.0.0" + }, + "PROTEUS": { + "r-base": "4.2.1", + "r-proteus-bartongroup": "0.2.16", + "r-plotly": "4.10.2", + "bioconductor-limma": "3.54.0" + }, + "VALIDATOR": { + "r-base": "4.3.3", + "r-shinyngs": "2.0.0" + }, + "Workflow": { + "nf-core/differentialabundance": "v1.6.0dev" + } + }, [ "other", "other/limma", @@ -147,6 +173,6 @@ "nf-test": "0.9.0", "nextflow": "24.10.0" }, - "timestamp": "2024-11-07T16:57:00.079425408" + "timestamp": "2024-11-17T21:32:05.655955914" } } \ No newline at end of file diff --git a/tests/test_nogtf.nf.test b/tests/test_nogtf.nf.test index ea685265..263513d2 100644 --- a/tests/test_nogtf.nf.test +++ b/tests/test_nogtf.nf.test @@ -24,6 +24,8 @@ nextflow_pipeline { { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/collated_versions.yml"), // All stable path name, with a relative path stable_name, // All files with stable contents diff --git a/tests/test_nogtf.nf.test.snap b/tests/test_nogtf.nf.test.snap index c07ecb96..ec570320 100644 --- a/tests/test_nogtf.nf.test.snap +++ b/tests/test_nogtf.nf.test.snap @@ -2,6 +2,26 @@ "Test no gtf profile": { "content": [ 13, + { + "DESEQ2_DIFFERENTIAL": { + "r-base": "4.1.3", + "bioconductor-deseq2": "1.34.0" + }, + "PLOT_DIFFERENTIAL": { + "r-base": "4.3.3", + "r-shinyngs": "2.0.0" + }, + "PLOT_EXPLORATORY": { + "r-shinyngs": "2.0.0" + }, + "VALIDATOR": { + "r-base": "4.3.3", + "r-shinyngs": "2.0.0" + }, + "Workflow": { + "nf-core/differentialabundance": "v1.6.0dev" + } + }, [ "other", "other/deseq2", @@ -82,6 +102,6 @@ "nf-test": "0.9.0", "nextflow": "24.10.0" }, - "timestamp": "2024-11-08T14:08:09.370720729" + "timestamp": "2024-11-17T21:34:30.304565869" } } \ No newline at end of file diff --git a/tests/test_rnaseq_limma.nf.test b/tests/test_rnaseq_limma.nf.test index 276d82c4..5139b177 100644 --- a/tests/test_rnaseq_limma.nf.test +++ b/tests/test_rnaseq_limma.nf.test @@ -24,6 +24,8 @@ nextflow_pipeline { { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/collated_versions.yml"), // All stable path name, with a relative path stable_name, // All files with stable contents diff --git a/tests/test_rnaseq_limma.nf.test.snap b/tests/test_rnaseq_limma.nf.test.snap index 3da2acf4..d3195034 100644 --- a/tests/test_rnaseq_limma.nf.test.snap +++ b/tests/test_rnaseq_limma.nf.test.snap @@ -2,6 +2,38 @@ "Test rnaseq limma profile": { "content": [ 20, + { + "GSEA_GSEA": { + "gsea": "4.3.2" + }, + "GTF_TO_TABLE": { + "atlas-gene-annotation-manipulation": "1.1.1" + }, + "GUNZIP_GTF": { + "gunzip": 1.1 + }, + "LIMMA_DIFFERENTIAL": { + "r-base": "4.3.3", + "bioconductor-limma": "3.58.1" + }, + "PLOT_DIFFERENTIAL": { + "r-base": "4.3.3", + "r-shinyngs": "2.0.0" + }, + "PLOT_EXPLORATORY": { + "r-shinyngs": "2.0.0" + }, + "TABULAR_TO_GSEA_CHIP": { + "bash": "4.2.25 3" + }, + "VALIDATOR": { + "r-base": "4.3.3", + "r-shinyngs": "2.0.0" + }, + "Workflow": { + "nf-core/differentialabundance": "v1.6.0dev" + } + }, [ "other", "other/limma", @@ -145,6 +177,6 @@ "nf-test": "0.9.0", "nextflow": "24.10.0" }, - "timestamp": "2024-11-08T13:12:28.480773381" + "timestamp": "2024-11-17T21:37:45.162699026" } } \ No newline at end of file diff --git a/tests/test_soft.nf.test b/tests/test_soft.nf.test index 92ed8af5..0d8b6605 100644 --- a/tests/test_soft.nf.test +++ b/tests/test_soft.nf.test @@ -24,6 +24,8 @@ nextflow_pipeline { { assert snapshot( // Number of successful tasks workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/collated_versions.yml"), // All stable path name, with a relative path stable_name, // All files with stable contents diff --git a/tests/test_soft.nf.test.snap b/tests/test_soft.nf.test.snap index f4db77b6..4f279620 100644 --- a/tests/test_soft.nf.test.snap +++ b/tests/test_soft.nf.test.snap @@ -2,6 +2,30 @@ "Test soft profile": { "content": [ 10, + { + "GEOQUERY_GETGEO": { + "r-base": "4.2.1", + "bioconductor-geoquery": "2.66.0" + }, + "LIMMA_DIFFERENTIAL": { + "r-base": "4.3.3", + "bioconductor-limma": "3.58.1" + }, + "PLOT_DIFFERENTIAL": { + "r-base": "4.3.3", + "r-shinyngs": "2.0.0" + }, + "PLOT_EXPLORATORY": { + "r-shinyngs": "2.0.0" + }, + "VALIDATOR": { + "r-base": "4.3.3", + "r-shinyngs": "2.0.0" + }, + "Workflow": { + "nf-core/differentialabundance": "v1.6.0dev" + } + }, [ "other", "other/affy", @@ -70,6 +94,6 @@ "nf-test": "0.9.0", "nextflow": "24.10.0" }, - "timestamp": "2024-11-08T14:12:26.809162392" + "timestamp": "2024-11-17T21:40:28.282036327" } } \ No newline at end of file From 1a3bbc7e01afbaae6702b5d237127b5076b96fec Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Sun, 17 Nov 2024 21:45:49 +0000 Subject: [PATCH 38/41] update changelog --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6bbc2f5c..f10a7aa1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,12 +7,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added +- [[#358](https://github.com/nf-core/differentialabundance/pull/358)] - Added software version check in nf-tests and gene biotype column check in `.Rmd` ([@atrigila](https://github.com/atrigila), review by [@pinin4fjords](https://github.com/pinin4fjords)) - [[#345](https://github.com/nf-core/differentialabundance/pull/345)] - Plot differentially expressed genes by gene biotype ([@atrigila](https://github.com/atrigila), review by [@grst](https://github.com/grst)) - [[#343](https://github.com/nf-core/differentialabundance/pull/343)] - Add pipeline-level nf-tests ([@atrigila](https://github.com/atrigila), review by [@pinin4fjords](https://github.com/pinin4fjords) and [@nschcolnicov](https://github.com/nschcolnicov)) - [[#286](https://github.com/nf-core/differentialabundance/pull/286)] - Integration of limma voom for rnaseq data ([@KamilMaliszArdigen](https://github.com/KamilMaliszArdigen), review by [@pinin4fjords](https://github.com/pinin4fjords)) ### Fixed +- [[#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)) - [[#344](https://github.com/nf-core/differentialabundance/pull/344)] - Fixed replacement of NA sub-strings ([@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)) - [[#342](https://github.com/nf-core/differentialabundance/pull/342)] - Fixed incorrectly colored dots in report volcano plots for logFC thresholds <1 ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords)) From 52f817e9e11721dd1d8cd903cd4f9cdd3a3232bb Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Tue, 19 Nov 2024 12:17:29 +0000 Subject: [PATCH 39/41] adjust indent --- assets/differentialabundance_report.Rmd | 43 ++++++++++++------------- 1 file changed, 21 insertions(+), 22 deletions(-) diff --git a/assets/differentialabundance_report.Rmd b/assets/differentialabundance_report.Rmd index 5e92e3c0..3ae5d8be 100644 --- a/assets/differentialabundance_report.Rmd +++ b/assets/differentialabundance_report.Rmd @@ -896,28 +896,27 @@ for (i in 1:nrow(contrasts)){ contrast_de <- round_dataframe_columns(contrast_de, digits=params$report_round_digits) print( htmltools::tagList(datatable(contrast_de, caption = paste('Differential genes', dir, 'in', contrast_descriptions[i], " (check", differential_files[[i]], "for more detail)"), rownames = FALSE) )) - # Check if Gene biotype column exists - if ("Gene biotype" %in% colnames(contrast_de)) { - # Plot Differentially Expressed Genes by Gene Biotype - gene_biotype_table <- contrast_de %>% - group_by(`Gene biotype`) %>% - summarise(count = dplyr::n(), .groups = 'drop') %>% - filter(count > 0) %>% - arrange(desc(count)) - - gene_biotype_plot <- ggplot(gene_biotype_table, aes(x = reorder(`Gene biotype`, -count), y = count)) + - geom_bar(stat = "identity", position = position_dodge()) + - labs( - title = paste0("Differentially Expressed Genes by Gene Biotype (", dir, ")"), - x = "Gene Biotype", - y = "Number of Differentially Expressed Genes" ) + - theme_minimal() + - theme(axis.text.x = element_text(angle = 45, hjust = 1)) - - print(gene_biotype_plot) - } else { - cat("Column 'Gene biotype' does not exist. Skipping plot.\n") - } + if ("Gene biotype" %in% colnames(contrast_de)) { + # Plot Differentially Expressed Genes by Gene Biotype + gene_biotype_table <- contrast_de %>% + group_by(`Gene biotype`) %>% + summarise(count = dplyr::n(), .groups = 'drop') %>% + filter(count > 0) %>% + arrange(desc(count)) + + gene_biotype_plot <- ggplot(gene_biotype_table, aes(x = reorder(`Gene biotype`, -count), y = count)) + + geom_bar(stat = "identity", position = position_dodge()) + + labs( + title = paste0("Differentially Expressed Genes by Gene Biotype (", dir, ")"), + x = "Gene Biotype", + y = "Number of Differentially Expressed Genes" ) + + theme_minimal() + + theme(axis.text.x = element_text(angle = 45, hjust = 1)) + + print(gene_biotype_plot) + } else { + cat("Column 'Gene biotype' does not exist. Skipping plot.\n") + } }else{ cat(paste0("No significantly differential '", dir, "' genes.\n\n")) } From be5172592f43d6df18b050ee1b745314cb13188d Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Tue, 19 Nov 2024 16:29:17 +0000 Subject: [PATCH 40/41] re-indent --- assets/differentialabundance_report.Rmd | 34 ++++++++++++------------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/assets/differentialabundance_report.Rmd b/assets/differentialabundance_report.Rmd index 3ae5d8be..6f79348d 100644 --- a/assets/differentialabundance_report.Rmd +++ b/assets/differentialabundance_report.Rmd @@ -897,23 +897,23 @@ for (i in 1:nrow(contrasts)){ print( htmltools::tagList(datatable(contrast_de, caption = paste('Differential genes', dir, 'in', contrast_descriptions[i], " (check", differential_files[[i]], "for more detail)"), rownames = FALSE) )) if ("Gene biotype" %in% colnames(contrast_de)) { - # Plot Differentially Expressed Genes by Gene Biotype - gene_biotype_table <- contrast_de %>% - group_by(`Gene biotype`) %>% - summarise(count = dplyr::n(), .groups = 'drop') %>% - filter(count > 0) %>% - arrange(desc(count)) - - gene_biotype_plot <- ggplot(gene_biotype_table, aes(x = reorder(`Gene biotype`, -count), y = count)) + - geom_bar(stat = "identity", position = position_dodge()) + - labs( - title = paste0("Differentially Expressed Genes by Gene Biotype (", dir, ")"), - x = "Gene Biotype", - y = "Number of Differentially Expressed Genes" ) + - theme_minimal() + - theme(axis.text.x = element_text(angle = 45, hjust = 1)) - - print(gene_biotype_plot) + # Plot Differentially Expressed Genes by Gene Biotype + gene_biotype_table <- contrast_de %>% + group_by(`Gene biotype`) %>% + summarise(count = dplyr::n(), .groups = 'drop') %>% + filter(count > 0) %>% + arrange(desc(count)) + + gene_biotype_plot <- ggplot(gene_biotype_table, aes(x = reorder(`Gene biotype`, -count), y = count)) + + geom_bar(stat = "identity", position = position_dodge()) + + labs( + title = paste0("Differentially Expressed Genes by Gene Biotype (", dir, ")"), + x = "Gene Biotype", + y = "Number of Differentially Expressed Genes" ) + + theme_minimal() + + theme(axis.text.x = element_text(angle = 45, hjust = 1)) + + print(gene_biotype_plot) } else { cat("Column 'Gene biotype' does not exist. Skipping plot.\n") } From e7fd0b49c335c9f6b45887013d58a5dc675a5474 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alan=20M=C3=B6bbs?= Date: Wed, 20 Nov 2024 12:18:48 +0000 Subject: [PATCH 41/41] Reduce code --- assets/differentialabundance_report.Rmd | 86 +++++++++---------------- 1 file changed, 30 insertions(+), 56 deletions(-) diff --git a/assets/differentialabundance_report.Rmd b/assets/differentialabundance_report.Rmd index e3eb0256..8babb4ba 100644 --- a/assets/differentialabundance_report.Rmd +++ b/assets/differentialabundance_report.Rmd @@ -375,11 +375,7 @@ warnings_list <- c() # Read differential results and merge with features table results <- lapply(differential_files, function(diff_file) { - warnings <- c() # Initialize local warning vector - - if (!file.exists(diff_file)) { - stop(paste("Differential file", diff_file, "does not exist")) - } + if (!file.exists(diff_file)) stop(paste("Differential file", diff_file, "does not exist")) diff <- read_differential( diff_file, @@ -389,65 +385,43 @@ results <- lapply(differential_files, function(diff_file) { qval_column = params$differential_qval_column ) - # If fold changes are not logged already, log them + # Log transform fold changes if not already logged if (!params$differential_foldchanges_logged) { diff[[params$differential_fc_column]] <- log2(diff[[params$differential_fc_column]]) } - # Annotate differential tables if possible + # Annotate differential table if features table is provided if (!is.null(params$features)) { - - # Merge tables - diff_features <- merge(features, diff, by.x = params$features_id_col, by.y = params$differential_feature_id_column) - - # Get number of rows before and after merging - rows_diff <- as.numeric(nrow(diff)) - rows_diff_features <- as.numeric(nrow(diff_features)) - - # Check that all IDs were conserved - conserved_ids <- all( diff[[params$differential_feature_id_column]] %in% diff_features[[params$features_id_col]] ) - - ## Check if all IDs are present - if (!conserved_ids) { - missing_ids <- setdiff(diff[[params$differential_feature_id_column]], diff_features[[params$features_id_col]]) - warnings <- c(warnings, - paste0( - '

WARNING:', length(missing_ids),' IDs from the differential expressed table (', basename(diff_file), ') were absent from the features table (', basename(params$features), ') and lost on merge.\n', - 'Missing IDs in diff table: ', paste(missing_ids, collapse = ' '), '.\n', - 'Rows in merged table: ', rows_diff_features, '.

\n' - ) + ## Merge Differential expression table on features table + merged <- merge(features, diff, by.x = params$features_id_col, by.y = params$differential_feature_id_column) + + ## Get number of missing rows + n_missing <- length(setdiff(diff[[params$differential_feature_id_column]], merged[[params$features_id_col]])) + + ## Create warnings if necessary + warnings <- c( + ## Missing IDs + if (n_missing > 0) sprintf( + '

WARNING: %d IDs from the differential table (%s) were lost on merge with features table (%s).

', + n_missing, basename(diff_file), basename(params$features) + ), + ## Check whether there are fewer rows, missing data + if (nrow(merged) < nrow(diff)) sprintf( + '

WARNING: Rows were lost on merge (%s -> %s). Original: %d, Merged: %d.

', + basename(diff_file), basename(params$features), nrow(diff), nrow(merged) + ), + ## Check whether there are more rows, possible duplications + if (nrow(merged) > nrow(diff)) sprintf( + '

WARNING: Rows were duplicated on merge (%s -> %s). Original: %d, Merged: %d.

', + basename(diff_file), basename(params$features), nrow(diff), nrow(merged) ) - } - - # Compare numbers and report - ## Check if features_diff has fewer rows, it would indicate lost of info - if ( rows_diff_features < rows_diff ) { - warnings <- c(warnings, - paste0( - '

WARNING: Some rows from the differential expressed table (', basename(diff_file), ') were absent from the features table (', basename(params$features), ') and lost on merge.\n', - 'Rows in diff table: ', rows_diff, '.\n', - 'Rows in merged table: ', rows_diff_features, '.

\n' - ) - ) - } - - ## Check if features_diff has more rows, it could indicate duplications - if ( rows_diff_features > rows_diff ) { - warnings <- c(warnings, - paste0( - '

WARNING: Some rows from the differential expressed table (', basename(diff_file), ') were duplicated on feature table (', basename(params$features), ').\n', - 'Rows in diff table: ', rows_diff, '.\n', - 'Rows in merged table: ', rows_diff_features, '.

\n' - ) - ) - } - + ) } else { - diff_features <- diff + merged <- diff + warnings <- character(0) } - - # Return both the results and the local warnings - list(diff_features = diff_features, warnings = warnings) + ## Collect results + list(diff_features = merged, warnings = warnings) }) # Separate differential_results and warnings_list from results