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Add software versions in nf-test and check column presence in .Rmd #359

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merged 6 commits into from
Nov 19, 2024
Merged

Add software versions in nf-test and check column presence in .Rmd #359

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4a3d212
always run tests
atrigila Nov 17, 2024
44a7330
check if column exists
atrigila Nov 17, 2024
f59c538
update tests with versions
atrigila Nov 17, 2024
1a3bbc7
update changelog
atrigila Nov 17, 2024
52f817e
adjust indent
atrigila Nov 19, 2024
be51725
re-indent
atrigila Nov 19, 2024
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1 change: 0 additions & 1 deletion .github/workflows/ci.yml
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Expand Up @@ -113,7 +113,6 @@ jobs:
nf-test test \
--ci \
--tag ${{matrix.test_profile}} \
--changed-since HEAD^ \
--profile "+${{ matrix.compute_profile }}" \
--junitxml=test.xml \
--debug
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -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))
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5 changes: 4 additions & 1 deletion assets/differentialabundance_report.Rmd
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Expand Up @@ -896,6 +896,7 @@ 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) ))

if ("Gene biotype" %in% colnames(contrast_de)) {
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# Plot Differentially Expressed Genes by Gene Biotype
gene_biotype_table <- contrast_de %>%
group_by(`Gene biotype`) %>%
Expand All @@ -913,7 +914,9 @@ for (i in 1:nrow(contrasts)){
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"))
}
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6 changes: 2 additions & 4 deletions tests/.nftignore
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Expand Up @@ -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}
2 changes: 2 additions & 0 deletions tests/test.nf.test
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Expand Up @@ -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
Expand Down
34 changes: 33 additions & 1 deletion tests/test.nf.test.snap
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Expand Up @@ -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",
Expand Down Expand Up @@ -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"
}
}
8 changes: 4 additions & 4 deletions tests/test_affy.nf.test
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Expand Up @@ -18,17 +18,17 @@ 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 ${params.outdir}/ with stable content
def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
assertAll(
{ assert workflow.success},
{ assert snapshot(
// Number of successful tasks
workflow.trace.succeeded().size(),
// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
removeNextflowVersion("$outputDir/pipeline_info/collated_versions.yml"),
// All stable path name, with a relative path
stable_name,
// All files with stable contents
Expand Down
32 changes: 31 additions & 1 deletion tests/test_affy.nf.test.snap
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Expand Up @@ -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",
Expand Down Expand Up @@ -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"
}
}
2 changes: 2 additions & 0 deletions tests/test_maxquant.nf.test
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Expand Up @@ -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("$outputDir/pipeline_info/collated_versions.yml"),
// All stable path name, with a relative path
stable_name,
// All files with stable contents
Expand Down
28 changes: 27 additions & 1 deletion tests/test_maxquant.nf.test.snap
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Expand Up @@ -2,6 +2,32 @@
"Test maxquant profile": {
"content": [
20,
{
"LIMMA_DIFFERENTIAL": {
"r-base": "4.3.3",
"bioconductor-limma": "3.58.1"
},
"PLOT_DIFFERENTIAL": {
"r-base": "4.3.3",
"r-shinyngs": "2.0.0"
},
"PLOT_EXPLORATORY": {
"r-shinyngs": "2.0.0"
},
"PROTEUS": {
"r-base": "4.2.1",
"r-proteus-bartongroup": "0.2.16",
"r-plotly": "4.10.2",
"bioconductor-limma": "3.54.0"
},
"VALIDATOR": {
"r-base": "4.3.3",
"r-shinyngs": "2.0.0"
},
"Workflow": {
"nf-core/differentialabundance": "v1.6.0dev"
}
},
[
"other",
"other/limma",
Expand Down Expand Up @@ -147,6 +173,6 @@
"nf-test": "0.9.0",
"nextflow": "24.10.0"
},
"timestamp": "2024-11-07T16:57:00.079425408"
"timestamp": "2024-11-17T21:32:05.655955914"
}
}
2 changes: 2 additions & 0 deletions tests/test_nogtf.nf.test
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Expand Up @@ -24,6 +24,8 @@ nextflow_pipeline {
{ assert snapshot(
// Number of successful tasks
workflow.trace.succeeded().size(),
// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
removeNextflowVersion("$outputDir/pipeline_info/collated_versions.yml"),
// All stable path name, with a relative path
stable_name,
// All files with stable contents
Expand Down
22 changes: 21 additions & 1 deletion tests/test_nogtf.nf.test.snap
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Expand Up @@ -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",
Expand Down Expand Up @@ -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"
}
}
2 changes: 2 additions & 0 deletions tests/test_rnaseq_limma.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -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("$outputDir/pipeline_info/collated_versions.yml"),
// All stable path name, with a relative path
stable_name,
// All files with stable contents
Expand Down
34 changes: 33 additions & 1 deletion tests/test_rnaseq_limma.nf.test.snap
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Expand Up @@ -2,6 +2,38 @@
"Test rnaseq limma profile": {
"content": [
20,
{
"GSEA_GSEA": {
"gsea": "4.3.2"
},
"GTF_TO_TABLE": {
"atlas-gene-annotation-manipulation": "1.1.1"
},
"GUNZIP_GTF": {
"gunzip": 1.1
},
"LIMMA_DIFFERENTIAL": {
"r-base": "4.3.3",
"bioconductor-limma": "3.58.1"
},
"PLOT_DIFFERENTIAL": {
"r-base": "4.3.3",
"r-shinyngs": "2.0.0"
},
"PLOT_EXPLORATORY": {
"r-shinyngs": "2.0.0"
},
"TABULAR_TO_GSEA_CHIP": {
"bash": "4.2.25 3"
},
"VALIDATOR": {
"r-base": "4.3.3",
"r-shinyngs": "2.0.0"
},
"Workflow": {
"nf-core/differentialabundance": "v1.6.0dev"
}
},
[
"other",
"other/limma",
Expand Down Expand Up @@ -145,6 +177,6 @@
"nf-test": "0.9.0",
"nextflow": "24.10.0"
},
"timestamp": "2024-11-08T13:12:28.480773381"
"timestamp": "2024-11-17T21:37:45.162699026"
}
}
2 changes: 2 additions & 0 deletions tests/test_soft.nf.test
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Expand Up @@ -24,6 +24,8 @@ nextflow_pipeline {
{ assert snapshot(
// Number of successful tasks
workflow.trace.succeeded().size(),
// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
removeNextflowVersion("$outputDir/pipeline_info/collated_versions.yml"),
// All stable path name, with a relative path
stable_name,
// All files with stable contents
Expand Down
26 changes: 25 additions & 1 deletion tests/test_soft.nf.test.snap
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Expand Up @@ -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",
Expand Down Expand Up @@ -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"
}
}
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