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antoniasaraccoantoniasaracco
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include decoupler testing
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‎tests/test_custom_paramsheet.nf.test.snap‎

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"nextflow": "25.04.3"
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},
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"timestamp": "2025-06-17T09:57:08.6693888"
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},
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"Test profile - with decoupler": {
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"content": [
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18,
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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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"DESEQ2_DIFFERENTIAL": {
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"r-base": "4.1.3",
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"bioconductor-deseq2": "1.34.0"
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},
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"DESEQ2_NORM": {
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"r-base": "4.1.3",
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"bioconductor-deseq2": "1.34.0"
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},
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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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"IMMUNEDECONV": {
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"r-immunedeconv": "2.1.0"
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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/deseq2",
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"other/deseq2/treatment_mCherry_hND6__SRP254919.dds.rld.rds",
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"other/deseq2/treatment_mCherry_hND6__SRP254919.deseq2.sizefactors.tsv",
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"other/deseq2/treatment_mCherry_hND6_sample_number_SRP254919.dds.rld.rds",
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"other/deseq2/treatment_mCherry_hND6_sample_number_SRP254919.deseq2.sizefactors.tsv",
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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/deseq2_treatment_mCherry_hND6__SRP254919_consensus_estimate_decoupler_plot.png",
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"plots/decoupler/deseq2_treatment_mCherry_hND6_sample_number_SRP254919_ulm_estimate_decoupler_plot.png",
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"plots/differential",
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"plots/differential/treatment_mCherry_hND6__SRP254919",
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"plots/differential/treatment_mCherry_hND6__SRP254919/png",
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"plots/differential/treatment_mCherry_hND6__SRP254919/png/volcano.png",
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"plots/differential/treatment_mCherry_hND6_sample_number_SRP254919/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/immunedeconv",
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"plots/immunedeconv/SRP254919.plot1_stacked_bar_chart.png",
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"plots/immunedeconv/SRP254919.plot2_points_with_facets.png",
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"plots/qc",
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"plots/qc/treatment_mCherry_hND6__SRP254919.deseq2.dispersion.png",
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"report",
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"report/SRP254919.zip",
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"shinyngs_app/SRP254919/app.R",
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"shinyngs_app/SRP254919/data.rds",
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"shinyngs_app/versions.yml",
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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/deseq2_treatment_mCherry_hND6__SRP254919_consensus_estimate_decoupler.tsv",
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"tables/decoupler/deseq2_treatment_mCherry_hND6__SRP254919_ulm_pvals_decoupler.tsv",
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"tables/decoupler/deseq2_treatment_mCherry_hND6_sample_number_SRP254919_ulm_estimate_decoupler.tsv",
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"tables/decoupler/deseq2_treatment_mCherry_hND6_sample_number_SRP254919_ulm_pvals_decoupler.tsv",
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"tables/differential",
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"tables/differential/treatment_mCherry_hND6__SRP254919.deseq2.results.tsv",
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"tables/differential/treatment_mCherry_hND6__SRP254919.deseq2.results_filtered.tsv",
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"tables/immunedeconv",
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"tables/immunedeconv/SRP254919.deconvolution_results.tsv",
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"tables/processed_abundance",
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"tables/processed_abundance/all.vst.tsv"
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],
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"SRP254919.deconvolution_results.tsv:md5,3d7ed4550a0da2f63fcfd2e74605e7a3",
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"all.normalised_counts.tsv:md5,f3ef0fb48f97afde2b5122b72dc4dcc4",
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"all.vst.tsv:md5,ae82509f76ed01ad0d041d1a62aef703"
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]
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],
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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": "2025-09-22T20:59:16.34498681"
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}
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}

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