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antoniasaraccoantoniasaracco
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Include decoupler testing
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‎tests/test_rnaseq_dream.nf.test‎

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@@ -67,4 +67,34 @@ nextflow_pipeline {
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}
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}
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test("Test rnaseq dream profile - with decoupler") {
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when {
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params {
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outdir = "$outputDir"
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functional_method = "decoupler"
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decoupler_min_n = 1
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}
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}
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then {
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// stable_name: All files + folders in ${params.outdir}/ with a stable name
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def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
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// stable_path: All files in ${params.outdir}/ with stable content
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def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
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assertAll(
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{ assert workflow.success},
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{ assert snapshot(
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// Number of successful tasks
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workflow.trace.succeeded().size(),
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// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
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removeNextflowVersion("$outputDir/pipeline_info/nf_core_differentialabundance_software_versions.yml"),
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// All stable path name, with a relative path
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stable_name,
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// All files with stable contents
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stable_path
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).match() }
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)
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}
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}
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}

‎tests/test_rnaseq_dream.nf.test.snap‎

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"nextflow": "25.04.6"
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},
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"timestamp": "2025-07-30T16:32:49.712383975"
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},
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"Test rnaseq dream profile - with decoupler": {
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"content": [
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13,
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{
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"CUSTOM_FILTERDIFFERENTIALTABLE": {
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"pandas": "1.5.2"
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},
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"DECOUPLER_DECOUPLER": null,
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"decoupler-py": "1.8.0",
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"GTF_TO_TABLE": {
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"atlas-gene-annotation-manipulation": "1.1.1"
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},
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"GUNZIP_GTF": {
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"gunzip": 1.1
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},
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"VALIDATOR": {
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"r-shinyngs": "2.2.4"
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},
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"VARIANCEPARTITION_DREAM": {
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"r-base": "4.3.3",
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"bioconductor-edger": "4.0.16",
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"variancePartition": "1.32.2"
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},
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"Workflow": {
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"nf-core/differentialabundance": "v1.6.0dev"
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}
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},
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[
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"pipeline_info",
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"pipeline_info/collated_versions.yml",
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"pipeline_info/nf_core_differentialabundance_software_versions.yml",
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"plots",
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"plots/decoupler",
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"plots/decoupler/dream_full_model_with_interactions_SRP254919_consensus_estimate_decoupler_plot.png",
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"plots/decoupler/dream_full_model_with_interactions_SRP254919_ulm_estimate_decoupler_plot.png",
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"plots/decoupler/dream_interaction_genotype_treatment_SRP254919_consensus_estimate_decoupler_plot.png",
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"plots/decoupler/dream_interaction_genotype_treatment_SRP254919_ulm_estimate_decoupler_plot.png",
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"plots/decoupler/dream_treatment_plus_genotype_SRP254919_consensus_estimate_decoupler_plot.png",
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"plots/decoupler/dream_treatment_plus_genotype_SRP254919_ulm_estimate_decoupler_plot.png",
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"tables",
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"tables/annotation",
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"tables/annotation/SRP254919.anno.tsv",
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"tables/decoupler",
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"tables/decoupler/dream_full_model_with_interactions_SRP254919_consensus_estimate_decoupler.tsv",
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"tables/decoupler/dream_full_model_with_interactions_SRP254919_consensus_pvals_decoupler.tsv",
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"tables/decoupler/dream_full_model_with_interactions_SRP254919_ulm_estimate_decoupler.tsv",
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"tables/decoupler/dream_full_model_with_interactions_SRP254919_ulm_pvals_decoupler.tsv",
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"tables/decoupler/dream_interaction_genotype_treatment_SRP254919_consensus_estimate_decoupler.tsv",
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"tables/decoupler/dream_interaction_genotype_treatment_SRP254919_consensus_pvals_decoupler.tsv",
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"tables/decoupler/dream_interaction_genotype_treatment_SRP254919_ulm_estimate_decoupler.tsv",
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"tables/decoupler/dream_interaction_genotype_treatment_SRP254919_ulm_pvals_decoupler.tsv",
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"tables/decoupler/dream_treatment_plus_genotype_SRP254919_consensus_estimate_decoupler.tsv",
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"tables/decoupler/dream_treatment_plus_genotype_SRP254919_consensus_pvals_decoupler.tsv",
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"tables/decoupler/dream_treatment_plus_genotype_SRP254919_ulm_estimate_decoupler.tsv",
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"tables/decoupler/dream_treatment_plus_genotype_SRP254919_ulm_pvals_decoupler.tsv",
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"tables/differential",
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"tables/differential/full_model_with_interactions_SRP254919.dream.results.tsv",
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"tables/differential/full_model_with_interactions_SRP254919.dream.results_filtered.tsv",
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"tables/differential/interaction_genotype_treatment_SRP254919.dream.results.tsv",
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"tables/differential/interaction_genotype_treatment_SRP254919.dream.results_filtered.tsv",
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"tables/differential/treatment_plus_genotype_SRP254919.dream.results.tsv",
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"tables/differential/treatment_plus_genotype_SRP254919.dream.results_filtered.tsv"
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],
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[
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"SRP254919.anno.tsv:md5,c1d7f21e64bd00f845ec6545c123a1fb",
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"dream_full_model_with_interactions_SRP254919_consensus_estimate_decoupler.tsv:md5,e362db3b7988a6cff9138c1f3f04e158",
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"dream_full_model_with_interactions_SRP254919_consensus_pvals_decoupler.tsv:md5,e0a6f2bac31c0009492607ffffe039b3",
169+
"dream_full_model_with_interactions_SRP254919_ulm_estimate_decoupler.tsv:md5,a4647244f62228f23dd181708ba524cb",
170+
"dream_full_model_with_interactions_SRP254919_ulm_pvals_decoupler.tsv:md5,c90af52101c49619540ac20adbdd4073",
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"dream_interaction_genotype_treatment_SRP254919_consensus_estimate_decoupler.tsv:md5,568545acb5825c2cf97a8c39462db454",
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"dream_interaction_genotype_treatment_SRP254919_consensus_pvals_decoupler.tsv:md5,efb57ded7d4f4c3256759cef4eddab57",
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"dream_interaction_genotype_treatment_SRP254919_ulm_estimate_decoupler.tsv:md5,33f600b2fbc46b9c7db4bd5c052b4be0",
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"dream_interaction_genotype_treatment_SRP254919_ulm_pvals_decoupler.tsv:md5,585b6c763eb86100f166adcb87a6ac7a",
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"dream_treatment_plus_genotype_SRP254919_consensus_estimate_decoupler.tsv:md5,32063dfe8ad7dd2a7fc36144b821150c",
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"dream_treatment_plus_genotype_SRP254919_consensus_pvals_decoupler.tsv:md5,e248178dd7d51916e088d3666d6435bd",
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"dream_treatment_plus_genotype_SRP254919_ulm_estimate_decoupler.tsv:md5,8337f5394f2bca6411f8e42fb51ea015",
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"dream_treatment_plus_genotype_SRP254919_ulm_pvals_decoupler.tsv:md5,d49131ebbabc8ddc737c106b60d41f7a"
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]
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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "25.04.7"
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},
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"timestamp": "2025-09-22T21:26:00.353247592"
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}
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}

‎tests/test_rnaseq_limma.nf.test‎

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@@ -100,4 +100,34 @@ nextflow_pipeline {
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)
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}
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}
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test("Test rnaseq limma profile - with decoupler") {
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when {
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params {
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outdir = "$outputDir"
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functional_method = "decoupler"
110+
}
111+
}
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then {
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// stable_name: All files + folders in ${params.outdir}/ with a stable name
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def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
116+
// stable_path: All files in ${params.outdir}/ with stable content
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def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
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assertAll(
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{ assert workflow.success},
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{ assert snapshot(
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// Number of successful tasks
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workflow.trace.succeeded().size(),
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// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
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removeNextflowVersion("$outputDir/pipeline_info/nf_core_differentialabundance_software_versions.yml"),
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// All stable path name, with a relative path
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stable_name,
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// All files with stable contents
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stable_path
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).match() }
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)
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}
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}
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}

‎tests/test_rnaseq_limma.nf.test.snap‎

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{
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"Test rnaseq limma profile - with decoupler": {
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"content": [
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17,
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{
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"CUSTOM_FILTERDIFFERENTIALTABLE": {
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"pandas": "1.5.2"
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},
9+
"DECOUPLER_DECOUPLER": null,
10+
"decoupler-py": "1.8.0",
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"GTF_TO_TABLE": {
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"atlas-gene-annotation-manipulation": "1.1.1"
13+
},
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"GUNZIP_GTF": {
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"gunzip": 1.1
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},
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"LIMMA_DIFFERENTIAL": {
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"r-base": "4.3.3",
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"bioconductor-limma": "3.58.1"
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},
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"LIMMA_NORM": {
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"r-base": "4.3.3",
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"bioconductor-limma": "3.58.1"
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},
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"PLOT_DIFFERENTIAL": {
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"r-shinyngs": "2.2.4"
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},
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"PLOT_EXPLORATORY": {
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"r-shinyngs": "2.2.4"
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},
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"SHINYNGS_APP": {
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"r-shinyngs": "2.2.4"
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},
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"VALIDATOR": {
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"r-shinyngs": "2.2.4"
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},
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"Workflow": {
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"nf-core/differentialabundance": "v1.6.0dev"
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}
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},
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[
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"other",
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"other/limma",
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"other/limma/treatment_mCherry_hND6__SRP254919.MArrayLM.limma.rds",
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"other/limma/treatment_mCherry_hND6_sample_number_SRP254919.MArrayLM.limma.rds",
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"pipeline_info",
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"pipeline_info/collated_versions.yml",
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"pipeline_info/nf_core_differentialabundance_software_versions.yml",
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"plots",
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"plots/decoupler",
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"plots/decoupler/limma_treatment_mCherry_hND6__SRP254919_consensus_estimate_decoupler_plot.png",
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"plots/decoupler/limma_treatment_mCherry_hND6__SRP254919_ulm_estimate_decoupler_plot.png",
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"plots/decoupler/limma_treatment_mCherry_hND6_sample_number_SRP254919_consensus_estimate_decoupler_plot.png",
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"plots/decoupler/limma_treatment_mCherry_hND6_sample_number_SRP254919_ulm_estimate_decoupler_plot.png",
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"plots/differential",
56+
"plots/differential/treatment_mCherry_hND6__SRP254919",
57+
"plots/differential/treatment_mCherry_hND6__SRP254919/png",
58+
"plots/differential/treatment_mCherry_hND6__SRP254919/png/volcano.png",
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"plots/differential/treatment_mCherry_hND6_sample_number_SRP254919",
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"plots/differential/treatment_mCherry_hND6_sample_number_SRP254919/png",
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"plots/differential/treatment_mCherry_hND6_sample_number_SRP254919/png/volcano.png",
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"plots/differential/versions.yml",
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"plots/exploratory",
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"plots/exploratory/treatment",
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"plots/exploratory/treatment/png",
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"plots/exploratory/treatment/png/boxplot.png",
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"plots/exploratory/treatment/png/density.png",
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"plots/exploratory/treatment/png/mad_correlation.png",
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"plots/exploratory/treatment/png/pca2d.png",
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"plots/exploratory/treatment/png/pca3d.png",
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"plots/exploratory/treatment/png/sample_dendrogram.png",
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"plots/exploratory/versions.yml",
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"plots/qc",
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"plots/qc/treatment_mCherry_hND6__SRP254919.limma.mean_difference.png",
75+
"plots/qc/treatment_mCherry_hND6_sample_number_SRP254919.limma.mean_difference.png",
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"report",
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"report/SRP254919.html",
78+
"report/SRP254919.zip",
79+
"shinyngs_app",
80+
"shinyngs_app/SRP254919",
81+
"shinyngs_app/SRP254919/app.R",
82+
"shinyngs_app/SRP254919/data.rds",
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"shinyngs_app/versions.yml",
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"tables",
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"tables/annotation",
86+
"tables/annotation/SRP254919.anno.tsv",
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"tables/decoupler",
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"tables/decoupler/limma_treatment_mCherry_hND6__SRP254919_consensus_estimate_decoupler.tsv",
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"tables/decoupler/limma_treatment_mCherry_hND6__SRP254919_consensus_pvals_decoupler.tsv",
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"tables/decoupler/limma_treatment_mCherry_hND6__SRP254919_ulm_estimate_decoupler.tsv",
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"tables/decoupler/limma_treatment_mCherry_hND6__SRP254919_ulm_pvals_decoupler.tsv",
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"tables/decoupler/limma_treatment_mCherry_hND6_sample_number_SRP254919_consensus_estimate_decoupler.tsv",
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"tables/decoupler/limma_treatment_mCherry_hND6_sample_number_SRP254919_consensus_pvals_decoupler.tsv",
94+
"tables/decoupler/limma_treatment_mCherry_hND6_sample_number_SRP254919_ulm_estimate_decoupler.tsv",
95+
"tables/decoupler/limma_treatment_mCherry_hND6_sample_number_SRP254919_ulm_pvals_decoupler.tsv",
96+
"tables/differential",
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"tables/differential/treatment_mCherry_hND6__SRP254919.limma.results.tsv",
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"tables/differential/treatment_mCherry_hND6__SRP254919.limma.results_filtered.tsv",
99+
"tables/differential/treatment_mCherry_hND6_sample_number_SRP254919.limma.results.tsv",
100+
"tables/differential/treatment_mCherry_hND6_sample_number_SRP254919.limma.results_filtered.tsv",
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"tables/processed_abundance",
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"tables/processed_abundance/all.normalised_counts.tsv"
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],
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[
105+
"versions.yml:md5,225ced8832439345efa781c726cf2e5c",
106+
"versions.yml:md5,d5f6ad8fe6242dcd75bc62b654d1d211",
107+
"app.R:md5,bedcfc45b6cdcc2b8fe3627987e2b17a",
108+
"versions.yml:md5,b3436c10ff83d0dab55060de3cae3ef2",
109+
"SRP254919.anno.tsv:md5,c1d7f21e64bd00f845ec6545c123a1fb",
110+
"limma_treatment_mCherry_hND6__SRP254919_consensus_estimate_decoupler.tsv:md5,a620d9e50bb80a940a1d625c156db57d",
111+
"limma_treatment_mCherry_hND6__SRP254919_consensus_pvals_decoupler.tsv:md5,0277a05f838537294818d929a00f3a51",
112+
"limma_treatment_mCherry_hND6__SRP254919_ulm_estimate_decoupler.tsv:md5,93e9f630eeb2b18aa7f9ee8368f87ae9",
113+
"limma_treatment_mCherry_hND6__SRP254919_ulm_pvals_decoupler.tsv:md5,5126f48f59bf1043076699f0677700bd",
114+
"limma_treatment_mCherry_hND6_sample_number_SRP254919_consensus_estimate_decoupler.tsv:md5,40d606009fd45e6e905b5c0284df720e",
115+
"limma_treatment_mCherry_hND6_sample_number_SRP254919_consensus_pvals_decoupler.tsv:md5,b58b5606148076511354925719d2476c",
116+
"limma_treatment_mCherry_hND6_sample_number_SRP254919_ulm_estimate_decoupler.tsv:md5,9156bed5878264a8ca2d543b3d2b73cf",
117+
"limma_treatment_mCherry_hND6_sample_number_SRP254919_ulm_pvals_decoupler.tsv:md5,b1eebaaa790893da0af00dc311a09236",
118+
"all.normalised_counts.tsv:md5,534f0f37e10325163656cad95418f34a"
119+
]
120+
],
121+
"meta": {
122+
"nf-test": "0.9.2",
123+
"nextflow": "25.04.7"
124+
},
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"timestamp": "2025-09-22T21:38:20.091516183"
126+
},
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"Test rnaseq limma profile": {
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"content": [
4129
22,

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