Update test snaps

nf-core · Dec 3, 2024 · 53257fb · 53257fb
1 parent f7db4ac
commit 53257fb
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Showing 4 changed files with 26 additions and 27 deletions.
diff --git a/tests/test.nf.test.snap b/tests/test.nf.test.snap
@@ -174,18 +174,18 @@
                 "app.R:md5,bedcfc45b6cdcc2b8fe3627987e2b17a",
                 "versions.yml:md5,892774f9d56ba10c8646736b7f777ecc",
                 "Mus_musculus.anno.tsv:md5,c1d7f21e64bd00f845ec6545c123a1fb",
-                "treatment_mCherry_hND6_.deseq2.results.tsv:md5,42ad391a5d3b2e4e7931af3088cc6400",
-                "treatment_mCherry_hND6_.deseq2.results_filtered.tsv:md5,cd67e101a9f0edf196ee0cd8491f8774",
-                "treatment_mCherry_hND6_sample_number.deseq2.results.tsv:md5,b41cbaacd04a25b45295f3f987ff7500",
-                "treatment_mCherry_hND6_sample_number.deseq2.results_filtered.tsv:md5,98fa3ec0992859d2a524ecce1259f0ed",
+                "treatment_mCherry_hND6_.deseq2.results.tsv:md5,b40bd97367cce0fc3926a722136bd936",
+                "treatment_mCherry_hND6_.deseq2.results_filtered.tsv:md5,b5560b6ccd18f09cb514d0b328448e0a",
+                "treatment_mCherry_hND6_sample_number.deseq2.results.tsv:md5,00303655a04cc0b3671932d6cb5011dc",
+                "treatment_mCherry_hND6_sample_number.deseq2.results_filtered.tsv:md5,08f3bb3a6c6abcd27c096f12c15c974c",
                 "all.normalised_counts.tsv:md5,1d7ad0c02b483f2eff1a5b357a74d011",
-                "all.vst.tsv:md5,a08d06d3c3218619b7bd85beead467bd"
+                "all.vst.tsv:md5,2fa9f1008e3536b049ca69d48bbe8fbd"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.10.0"
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-17T21:24:54.504828126"
+        "timestamp": "2024-12-03T17:05:32.173242283"
     }
 }
diff --git a/tests/test_affy.nf.test.snap b/tests/test_affy.nf.test.snap
@@ -35,7 +35,7 @@
             [
                 "other",
                 "other/affy",
-                "other/affy/raw.eset.rds",
+                "other/affy/raw._eset.rds",
                 "other/limma",
                 "other/limma/phenotype_uninvolved_lesional.MArrayLM.limma.rds",
                 "pipeline_info",
@@ -71,6 +71,8 @@
                 "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_ALLOGRAFT_REJECTION.tsv",
                 "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_ANGIOGENESIS.html",
+                "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_ANGIOGENESIS.tsv",
                 "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_APICAL_JUNCTION.html",
                 "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_APICAL_JUNCTION.tsv",
                 "report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_APOPTOSIS.html",
@@ -156,8 +158,6 @@
                 "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",
-                "tables/processed_abundance/raw.matrix.tsv",
                 "untar",
                 "untar/GSE50790",
                 "untar/GSE50790/GSM1229341_Gudjohnsson_001_6690_PP.CEL.gz",
@@ -170,7 +170,7 @@
                 "untar/GSE50790/GSM1229348_Gudjohnsson_008_8470_PN.CEL.gz"
             ],
             [
-                "raw.eset.rds:md5,8c6c7807ce6c5d8204bd681b941eeb0f",
+                "raw._eset.rds:md5,8c6c7807ce6c5d8204bd681b941eeb0f",
                 "phenotype_uninvolved_lesional.MArrayLM.limma.rds:md5,b5ef9fc63c87a83bf925f9284d83663f",
                 "volcano.png:md5,d4381dd34786c58e25b8e4ed1fa8bf26",
                 "versions.yml:md5,b20728a34a3537e339078bbeaababee9",
@@ -185,6 +185,7 @@
                 "phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_ADIPOGENESIS.tsv:md5,6dcf05651f6b0386fe089eaa421c3127",
                 "phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_ALLOGRAFT_REJECTION.tsv:md5,e9dd4c2530785273c996dbf8e989e4cb",
                 "phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_ANDROGEN_RESPONSE.tsv:md5,ed31e69bedf9bfdef793db64f60e0e3d",
+                "phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_ANGIOGENESIS.tsv:md5,0742906e4fbdd02a37151f55ee2db847",
                 "phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_APICAL_JUNCTION.tsv:md5,b7ffdef669d6e8a7d6065b0ee4d94f08",
                 "phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_APOPTOSIS.tsv:md5,6ce114c47b7c57eb2713e7b193b42561",
                 "phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_BILE_ACID_METABOLISM.tsv:md5,802fc042c26bdcabe683df4597c0086e",
@@ -224,8 +225,6 @@
                 "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",
@@ -238,8 +237,8 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.10.0"
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-17T21:29:47.480048632"
+        "timestamp": "2024-12-03T17:59:15.829545504"
     }
 }
diff --git a/tests/test_nogtf.nf.test.snap b/tests/test_nogtf.nf.test.snap
@@ -90,18 +90,18 @@
                 "treatment_mCherry_hND6_sample_number.deseq2.dispersion.png:md5,d0f07f97c7f5c660b173d85b85ed50b9",
                 "app.R:md5,bedcfc45b6cdcc2b8fe3627987e2b17a",
                 "versions.yml:md5,892774f9d56ba10c8646736b7f777ecc",
-                "treatment_mCherry_hND6_.deseq2.results.tsv:md5,d9e894aeb89aa5bc79bf7ce31304d7c0",
-                "treatment_mCherry_hND6_.deseq2.results_filtered.tsv:md5,630820ec91287d8bcb2e5882431c09c3",
-                "treatment_mCherry_hND6_sample_number.deseq2.results.tsv:md5,02b1c8f3c2987b0cb1a64913dd90bf26",
-                "treatment_mCherry_hND6_sample_number.deseq2.results_filtered.tsv:md5,1e1c8edb0aa5acee308bc1fc81d1aa16",
+                "treatment_mCherry_hND6_.deseq2.results.tsv:md5,4726dd3c33edce84d6356079c578bbd4",
+                "treatment_mCherry_hND6_.deseq2.results_filtered.tsv:md5,5c23f53046190eabce927cc968abed34",
+                "treatment_mCherry_hND6_sample_number.deseq2.results.tsv:md5,119c986fd9235ae6a6c88ed1dd4d0a3d",
+                "treatment_mCherry_hND6_sample_number.deseq2.results_filtered.tsv:md5,6d969a3049ba16f8f12fc8abeb2b9899",
                 "all.normalised_counts.tsv:md5,e960aa685547a3ea778523da84fae136",
-                "all.vst.tsv:md5,ea4e437ee57b2c5ef8c19d427656e3c6"
+                "all.vst.tsv:md5,8e19361180daa5a68de6f099b9093a8c"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.10.0"
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-17T21:34:30.304565869"
+        "timestamp": "2024-12-03T17:13:45.527625008"
     }
 }
diff --git a/tests/test_soft.nf.test.snap b/tests/test_soft.nf.test.snap
@@ -4,8 +4,8 @@
             10,
             {
                 "GEOQUERY_GETGEO": {
-                    "r-base": "4.2.1",
-                    "bioconductor-geoquery": "2.66.0"
+                    "r-base": "4.3.2",
+                    "bioconductor-geoquery": "2.70.0"
                 },
                 "LIMMA_DIFFERENTIAL": {
                     "r-base": "4.3.3",
@@ -70,7 +70,7 @@
                 "tables/processed_abundance/normalised.matrix.tsv"
             ],
             [
-                "normalised.eset.rds:md5,7f17b964d5a7b369767910635dfa23d7",
+                "normalised.eset.rds:md5,ee83ece8b75d711163af9dd9300db49a",
                 "phenotype_uninvolved_lesional.MArrayLM.limma.rds:md5,eecc9b0267ce9a5d3a1330da7fbce4cc",
                 "volcano.png:md5,18e35512a52ff82be16cc14330c1ac89",
                 "versions.yml:md5,b20728a34a3537e339078bbeaababee9",
@@ -92,8 +92,8 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.10.0"
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-17T21:40:28.282036327"
+        "timestamp": "2024-12-03T17:18:11.428945243"
     }
 }