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update snapshots
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-6
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‎tests/default.nf.test.snap‎

Lines changed: 35 additions & 3 deletions
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@@ -451,7 +451,11 @@
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"other/gprofiler2/full_model_with_interactions_SRP254919",
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"other/gprofiler2/interaction_genotype_treatment_SRP254919",
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"other/gprofiler2/treatment_effect_classic_comparison_SRP254919",
454+
"other/gprofiler2/treatment_effect_classic_comparison_SRP254919.gprofiler2.gost_results.rds",
455+
"other/gprofiler2/treatment_effect_classic_comparison_SRP254919/treatment_effect_classic_comparison_SRP254919.gprofiler2.gost_results.rds",
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"other/gprofiler2/treatment_plus_genotype_SRP254919",
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"other/gprofiler2/treatment_plus_genotype_SRP254919.gprofiler2.gost_results.rds",
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"other/gprofiler2/treatment_plus_genotype_SRP254919/treatment_plus_genotype_SRP254919.gprofiler2.gost_results.rds",
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"pipeline_info",
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"pipeline_info/collated_versions.yml",
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"pipeline_info/nf_core_differentialabundance_software_versions.yml",
@@ -484,7 +488,17 @@
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"plots/gprofiler2/full_model_with_interactions_SRP254919",
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"plots/gprofiler2/interaction_genotype_treatment_SRP254919",
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"plots/gprofiler2/treatment_effect_classic_comparison_SRP254919",
491+
"plots/gprofiler2/treatment_effect_classic_comparison_SRP254919/treatment_effect_classic_comparison_SRP254919.gprofiler2.CORUM.sub_enriched_pathways.png",
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"plots/gprofiler2/treatment_effect_classic_comparison_SRP254919/treatment_effect_classic_comparison_SRP254919.gprofiler2.HP.sub_enriched_pathways.png",
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"plots/gprofiler2/treatment_effect_classic_comparison_SRP254919/treatment_effect_classic_comparison_SRP254919.gprofiler2.REAC.sub_enriched_pathways.png",
495+
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"plots/gprofiler2/treatment_effect_classic_comparison_SRP254919/treatment_effect_classic_comparison_SRP254919.gprofiler2.gostplot.png",
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"plots/gprofiler2/treatment_plus_genotype_SRP254919",
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"plots/gprofiler2/treatment_plus_genotype_SRP254919/treatment_plus_genotype_SRP254919.gprofiler2.HP.sub_enriched_pathways.png",
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"plots/gprofiler2/treatment_plus_genotype_SRP254919/treatment_plus_genotype_SRP254919.gprofiler2.TF.sub_enriched_pathways.png",
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"plots/gprofiler2/treatment_plus_genotype_SRP254919/treatment_plus_genotype_SRP254919.gprofiler2.gostplot.html",
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"plots/gprofiler2/treatment_plus_genotype_SRP254919/treatment_plus_genotype_SRP254919.gprofiler2.gostplot.png",
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"plots/qc",
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"plots/qc/full_model_with_interactions_SRP254919.deseq2.dispersion.png",
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"plots/qc/interaction_genotype_treatment_SRP254919.deseq2.dispersion.png",
@@ -513,8 +527,14 @@
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"tables/gprofiler2/interaction_genotype_treatment_SRP254919",
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"tables/gprofiler2/interaction_genotype_treatment_SRP254919/interaction_genotype_treatment_SRP254919.gprofiler2.all_enriched_pathways.tsv",
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"tables/gprofiler2/treatment_effect_classic_comparison_SRP254919",
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531+
"tables/gprofiler2/treatment_effect_classic_comparison_SRP254919/treatment_effect_classic_comparison_SRP254919.gprofiler2.HP.sub_enriched_pathways.tsv",
532+
"tables/gprofiler2/treatment_effect_classic_comparison_SRP254919/treatment_effect_classic_comparison_SRP254919.gprofiler2.KEGG.sub_enriched_pathways.tsv",
533+
"tables/gprofiler2/treatment_effect_classic_comparison_SRP254919/treatment_effect_classic_comparison_SRP254919.gprofiler2.REAC.sub_enriched_pathways.tsv",
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"tables/gprofiler2/treatment_plus_genotype_SRP254919",
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"tables/gprofiler2/treatment_plus_genotype_SRP254919/treatment_plus_genotype_SRP254919.gprofiler2.HP.sub_enriched_pathways.tsv",
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"tables/processed_abundance",
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"tables/processed_abundance/all.normalised_counts.tsv",
@@ -525,8 +545,14 @@
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548+
"treatment_effect_classic_comparison_SRP254919.gprofiler2.gost_results.rds:md5,f998063c30498a5d38398be25f9d0c60",
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"treatment_effect_classic_comparison_SRP254919.gprofiler2.gost_results.rds:md5,f998063c30498a5d38398be25f9d0c60",
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"treatment_plus_genotype_SRP254919.gprofiler2.gost_results.rds:md5,d15ce1e767bf360711d67618244b750b",
551+
"treatment_plus_genotype_SRP254919.gprofiler2.gost_results.rds:md5,d15ce1e767bf360711d67618244b750b",
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"versions.yml:md5,225ced8832439345efa781c726cf2e5c",
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554+
"treatment_effect_classic_comparison_SRP254919.gprofiler2.gostplot.html:md5,24d0f1b4906121e900f95da1523706a0",
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"treatment_plus_genotype_SRP254919.gprofiler2.gostplot.html:md5,eeb4cc75c076e26f2ae62fb3de485536",
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"app.R:md5,bedcfc45b6cdcc2b8fe3627987e2b17a",
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"SRP254919.anno.tsv:md5,c1d7f21e64bd00f845ec6545c123a1fb",
@@ -538,8 +564,14 @@
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"treatment_effect_classic_comparison_SRP254919.deseq2.results_filtered.tsv:md5,65e7a9d354eb71db7f13576cc2d5d7e7",
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"full_model_with_interactions_SRP254919.gprofiler2.all_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
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"interaction_genotype_treatment_SRP254919.gprofiler2.all_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
541-
"treatment_effect_classic_comparison_SRP254919.gprofiler2.all_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
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"treatment_plus_genotype_SRP254919.gprofiler2.all_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
567+
"treatment_effect_classic_comparison_SRP254919.gprofiler2.CORUM.sub_enriched_pathways.tsv:md5,d7dca3803318350b7d3328dc14e8846b",
568+
"treatment_effect_classic_comparison_SRP254919.gprofiler2.HP.sub_enriched_pathways.tsv:md5,6c2249f6a9b4eb5ee0168fa44a670dea",
569+
"treatment_effect_classic_comparison_SRP254919.gprofiler2.KEGG.sub_enriched_pathways.tsv:md5,58c77b638e8b4e02cd486cf6b03d5ab6",
570+
"treatment_effect_classic_comparison_SRP254919.gprofiler2.REAC.sub_enriched_pathways.tsv:md5,0790f8beea2055f927741b27eb675e7b",
571+
"treatment_effect_classic_comparison_SRP254919.gprofiler2.all_enriched_pathways.tsv:md5,7988d05d69d9f17b654d4a8a514fa5c7",
572+
"treatment_plus_genotype_SRP254919.gprofiler2.HP.sub_enriched_pathways.tsv:md5,1e67df6e7e51f8d733714e25d61db06d",
573+
"treatment_plus_genotype_SRP254919.gprofiler2.TF.sub_enriched_pathways.tsv:md5,704e772ab4c6b8e6768d7dd8abb370bd",
574+
"treatment_plus_genotype_SRP254919.gprofiler2.all_enriched_pathways.tsv:md5,9cf6caebcf0b59460cefc5d3532207ee",
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"all.normalised_counts.tsv:md5,c2d7cc11637ad01ea49fff4a744965c9",
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"all.rlog.tsv:md5,bce2521996537372c72f4083f66c5d3b"
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]
@@ -548,7 +580,7 @@
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"nf-test": "0.9.2",
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"nextflow": "25.04.6"
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},
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"timestamp": "2025-07-24T16:46:01.377784674"
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"timestamp": "2025-09-03T15:56:00.993083639"
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},
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"Test profile - yml no formula": {
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"content": [

‎tests/test_custom_paramsheet.nf.test.snap‎

Lines changed: 16 additions & 3 deletions
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@@ -53,6 +53,8 @@
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"other/gprofiler2",
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"other/gprofiler2/treatment_mCherry_hND6__SRP254919",
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"other/gprofiler2/treatment_mCherry_hND6_sample_number_SRP254919",
56+
"other/gprofiler2/treatment_mCherry_hND6_sample_number_SRP254919.gprofiler2.gost_results.rds",
57+
"other/gprofiler2/treatment_mCherry_hND6_sample_number_SRP254919/treatment_mCherry_hND6_sample_number_SRP254919.gprofiler2.gost_results.rds",
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"pipeline_info",
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"pipeline_info/collated_versions.yml",
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"pipeline_info/nf_core_differentialabundance_software_versions.yml",
@@ -78,6 +80,10 @@
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"plots/gprofiler2",
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"plots/gprofiler2/treatment_mCherry_hND6__SRP254919",
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"plots/gprofiler2/treatment_mCherry_hND6_sample_number_SRP254919",
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"plots/gprofiler2/treatment_mCherry_hND6_sample_number_SRP254919/treatment_mCherry_hND6_sample_number_SRP254919.gprofiler2.GO:CC.sub_enriched_pathways.png",
84+
"plots/gprofiler2/treatment_mCherry_hND6_sample_number_SRP254919/treatment_mCherry_hND6_sample_number_SRP254919.gprofiler2.GO:MF.sub_enriched_pathways.png",
85+
"plots/gprofiler2/treatment_mCherry_hND6_sample_number_SRP254919/treatment_mCherry_hND6_sample_number_SRP254919.gprofiler2.gostplot.html",
86+
"plots/gprofiler2/treatment_mCherry_hND6_sample_number_SRP254919/treatment_mCherry_hND6_sample_number_SRP254919.gprofiler2.gostplot.png",
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"plots/immunedeconv",
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"plots/immunedeconv/SRP254919.plot1_stacked_bar_chart.png",
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"plots/immunedeconv/SRP254919.plot2_points_with_facets.png",
@@ -104,6 +110,8 @@
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"tables/gprofiler2/treatment_mCherry_hND6__SRP254919",
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"tables/gprofiler2/treatment_mCherry_hND6__SRP254919/treatment_mCherry_hND6__SRP254919.gprofiler2.all_enriched_pathways.tsv",
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"tables/gprofiler2/treatment_mCherry_hND6_sample_number_SRP254919",
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"tables/gprofiler2/treatment_mCherry_hND6_sample_number_SRP254919/treatment_mCherry_hND6_sample_number_SRP254919.gprofiler2.GO:CC.sub_enriched_pathways.tsv",
114+
"tables/gprofiler2/treatment_mCherry_hND6_sample_number_SRP254919/treatment_mCherry_hND6_sample_number_SRP254919.gprofiler2.GO:MF.sub_enriched_pathways.tsv",
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"tables/gprofiler2/treatment_mCherry_hND6_sample_number_SRP254919/treatment_mCherry_hND6_sample_number_SRP254919.gprofiler2.all_enriched_pathways.tsv",
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"tables/immunedeconv",
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"tables/immunedeconv/SRP254919.deconvolution_results.tsv",
@@ -114,8 +122,11 @@
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[
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"treatment_mCherry_hND6__SRP254919.deseq2.sizefactors.tsv:md5,0703c421c53b260f91568dfc0436c054",
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"treatment_mCherry_hND6_sample_number_SRP254919.deseq2.sizefactors.tsv:md5,0703c421c53b260f91568dfc0436c054",
125+
"treatment_mCherry_hND6_sample_number_SRP254919.gprofiler2.gost_results.rds:md5,9f987c1af30854a741f69d8f2e467cbb",
126+
"treatment_mCherry_hND6_sample_number_SRP254919.gprofiler2.gost_results.rds:md5,9f987c1af30854a741f69d8f2e467cbb",
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"versions.yml:md5,d5f6ad8fe6242dcd75bc62b654d1d211",
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"treatment_mCherry_hND6_sample_number_SRP254919.gprofiler2.gostplot.html:md5,b67f62775180ba244a82741324040b03",
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@@ -124,17 +135,19 @@
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"treatment_mCherry_hND6_sample_number_SRP254919.deseq2.results_filtered.tsv:md5,c88d36f46f7d8a4dd8c169c249f50540",
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"treatment_mCherry_hND6__SRP254919.gprofiler2.all_enriched_pathways.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
127-
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"treatment_mCherry_hND6_sample_number_SRP254919.gprofiler2.GO:CC.sub_enriched_pathways.tsv:md5,a7127a9491097019d3d6bb53cb00ec8e",
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"treatment_mCherry_hND6_sample_number_SRP254919.gprofiler2.GO:MF.sub_enriched_pathways.tsv:md5,fc811363bc5cd3196d88906a06e20419",
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"treatment_mCherry_hND6_sample_number_SRP254919.gprofiler2.all_enriched_pathways.tsv:md5,3b069b57f1043fa5b700abeec0b28e73",
128141
"SRP254919.deconvolution_results.tsv:md5,3d7ed4550a0da2f63fcfd2e74605e7a3",
129142
"all.normalised_counts.tsv:md5,f3ef0fb48f97afde2b5122b72dc4dcc4",
130143
"all.vst.tsv:md5,ae82509f76ed01ad0d041d1a62aef703"
131144
]
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],
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"meta": {
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"nf-test": "0.9.2",
135-
"nextflow": "25.04.3"
148+
"nextflow": "25.04.6"
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},
137-
"timestamp": "2025-06-17T09:59:11.644008654"
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"timestamp": "2025-09-03T15:30:52.476965842"
138151
},
139152
"Test profile - deseq2": {
140153
"content": [

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