tests: remove unstable rds file

atrigila · atrigila · commit c00e474aa308 · 2025-05-02T20:26:46.000Z
diff --git a/tests/.nftignore b/tests/.nftignore
@@ -92,3 +92,4 @@ umitools/*.umi_extract.log
 {salmon,star_salmon}/*/quant.genes.sf
 {salmon,star_salmon}/*/quant.sf
 {salmon,star_salmon}/salmon.*
+{salmon,kallisto}/all_samples_{gene,transcript}.SummarizedExperiment.rds
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
@@ -1386,8 +1386,6 @@
                 "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
                 "cmd_info.json:md5,fe66c9d876645b9260d8c2488157d4d4",
                 "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400",
-                "all_samples_gene.SummarizedExperiment.rds:md5,b1b1ba0badb98b9f2c183624486fb0bb",
-                "all_samples_transcript.SummarizedExperiment.rds:md5,771ba1d308a99d94210a0627e905225d",
                 "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676",
                 "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe",
                 "ambig_info.tsv:md5,f9a605d54a0a103566f7a9b8e0867a73",
@@ -1493,6 +1491,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.6"
         },
-        "timestamp": "2025-05-02T15:58:53.501817584"
+        "timestamp": "2025-05-02T18:28:55.976743746"
     }
 }
diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap
@@ -1351,8 +1351,6 @@
                 "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
                 "cmd_info.json:md5,fe66c9d876645b9260d8c2488157d4d4",
                 "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400",
-                "all_samples_gene.SummarizedExperiment.rds:md5,a6ad99dcab8929853732438e10e41127",
-                "all_samples_transcript.SummarizedExperiment.rds:md5,dc35a2d6b5e9f090bf4acb49a1fa15f8",
                 "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676",
                 "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe",
                 "ambig_info.tsv:md5,f9a605d54a0a103566f7a9b8e0867a73",
@@ -1443,6 +1441,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.6"
         },
-        "timestamp": "2025-05-02T16:08:01.437638477"
+        "timestamp": "2025-05-02T18:43:19.966299161"
     }
 }
diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap
@@ -1336,8 +1336,6 @@
                 "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
                 "cmd_info.json:md5,fe66c9d876645b9260d8c2488157d4d4",
                 "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400",
-                "all_samples_gene.SummarizedExperiment.rds:md5,b888784394518aeb1658ed87ac75b0aa",
-                "all_samples_transcript.SummarizedExperiment.rds:md5,c2547a0f0e65ed6339c38f5d9f9a6753",
                 "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676",
                 "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe"
             ]
@@ -1346,6 +1344,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.6"
         },
-        "timestamp": "2025-05-02T16:16:11.524273892"
+        "timestamp": "2025-05-02T18:55:20.186245374"
     }
 }
diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap
@@ -254,8 +254,6 @@
             [
                 "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055",
                 "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28",
-                "all_samples_gene.SummarizedExperiment.rds:md5,6f402b9130a73a3658ba1b2325505619",
-                "all_samples_transcript.SummarizedExperiment.rds:md5,873143aeeb41941ec6cc7ea7749ffd28",
                 "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe",
                 "cutadapt_filtered_reads_plot.txt:md5,6fa381627f7c1f664f3d4b2cb79cce90",
                 "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f",
@@ -279,7 +277,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.6"
         },
-        "timestamp": "2025-05-02T16:21:02.12262366"
+        "timestamp": "2025-05-02T19:02:06.6706681"
     },
     "Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub": {
         "content": [
diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap
@@ -1117,8 +1117,6 @@
                 "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
                 "cmd_info.json:md5,fe66c9d876645b9260d8c2488157d4d4",
                 "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400",
-                "all_samples_gene.SummarizedExperiment.rds:md5,bdaf6706240653e5cc0deaec5d26dcd2",
-                "all_samples_transcript.SummarizedExperiment.rds:md5,1495b9d7e65846df23acad7782ab3435",
                 "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676",
                 "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe",
                 "ambig_info.tsv:md5,f9a605d54a0a103566f7a9b8e0867a73",
@@ -1198,7 +1196,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.6"
         },
-        "timestamp": "2025-05-02T16:30:42.915343274"
+        "timestamp": "2025-05-02T19:13:23.557869665"
     },
     "Params: --min_mapped_reads 90 - stub": {
         "content": [
diff --git a/tests/nofasta.nf.test.snap b/tests/nofasta.nf.test.snap
@@ -417,8 +417,6 @@
                 "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
                 "cmd_info.json:md5,3e6d06d032abd3f5cd7e79df1b5bcde0",
                 "lib_format_counts.json:md5,fce2c4840048c294c016f45f0df15384",
-                "all_samples_gene.SummarizedExperiment.rds:md5,9374be23b333ce1cd865e7baf3d3c9cc",
-                "all_samples_transcript.SummarizedExperiment.rds:md5,5887511793e75ecd158e295a66e001d6",
                 "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676",
                 "tx2gene.tsv:md5,1be389a28cc26d94b19ea918959ac72e"
             ]
@@ -427,6 +425,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.6"
         },
-        "timestamp": "2025-05-02T16:34:02.48152685"
+        "timestamp": "2025-05-02T19:16:45.468836741"
     }
 }
diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap
@@ -1302,8 +1302,6 @@
                 "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
                 "cmd_info.json:md5,fa7b659f1ba90e16b0d0a375ff318b01",
                 "lib_format_counts.json:md5,e6e3d7746e9abee6a0e097ae0ee1781a",
-                "all_samples_gene.SummarizedExperiment.rds:md5,9dcce8af9916a0b1e6be6f99352ac57d",
-                "all_samples_transcript.SummarizedExperiment.rds:md5,f52c091d9af2a014d33a77dbd7f4bddd",
                 "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676",
                 "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe",
                 "ambig_info.tsv:md5,6cd02367152bb2dd59a6f1f70df2d7f8",
@@ -1409,7 +1407,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.6"
         },
-        "timestamp": "2025-05-02T16:46:56.051415315"
+        "timestamp": "2025-05-02T19:31:53.045728631"
     },
     "Params: --remove_ribo_rna - stub": {
         "content": [
diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap
@@ -346,16 +346,14 @@
                 "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
                 "cmd_info.json:md5,fe66c9d876645b9260d8c2488157d4d4",
                 "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400",
-                "all_samples_gene.SummarizedExperiment.rds:md5,d8d958d0e4dc43b128a3ea1e85a5556f",
-                "all_samples_transcript.SummarizedExperiment.rds:md5,b708a0313e3bc5853d597bad9ba595d9",
                 "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.6"
         },
-        "timestamp": "2025-05-02T16:51:23.617475353"
+        "timestamp": "2025-05-02T19:38:03.700997798"
     },
     "Params: --pseudo_aligner salmon --skip_qc --skip_alignment - stub": {
         "content": [
diff --git a/tests/skip_qc.nf.test.snap b/tests/skip_qc.nf.test.snap
@@ -761,8 +761,6 @@
                 "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
                 "cmd_info.json:md5,fe66c9d876645b9260d8c2488157d4d4",
                 "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400",
-                "all_samples_gene.SummarizedExperiment.rds:md5,32120e24c1b7e4e810b729e4f262d5f3",
-                "all_samples_transcript.SummarizedExperiment.rds:md5,050ab2685cfe3508691f9ed47edfaf6f",
                 "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe",
                 "ambig_info.tsv:md5,f9a605d54a0a103566f7a9b8e0867a73",
                 "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
@@ -821,6 +819,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.6"
         },
-        "timestamp": "2025-05-02T16:58:21.475263764"
+        "timestamp": "2025-05-02T19:46:18.144171012"
     }
 }
diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap
@@ -1166,8 +1166,6 @@
                 "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
                 "cmd_info.json:md5,fe66c9d876645b9260d8c2488157d4d4",
                 "lib_format_counts.json:md5,4bf135c93c37f90c493f761f2709a28b",
-                "all_samples_gene.SummarizedExperiment.rds:md5,3bdcf550efffa0700e7a5400fcde5662",
-                "all_samples_transcript.SummarizedExperiment.rds:md5,76d729c0a357e66483763b8f8397aefe",
                 "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676",
                 "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe",
                 "ambig_info.tsv:md5,d1d3bd2a5617220b29a9063cb29f0578",
@@ -1273,6 +1271,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.6"
         },
-        "timestamp": "2025-05-02T17:08:51.512966882"
+        "timestamp": "2025-05-02T19:57:03.409484347"
     }
 }
diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap
@@ -1216,8 +1216,6 @@
                 "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
                 "cmd_info.json:md5,fe66c9d876645b9260d8c2488157d4d4",
                 "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400",
-                "all_samples_gene.SummarizedExperiment.rds:md5,f1d87dbdc3f7523115d4c90f716a7adf",
-                "all_samples_transcript.SummarizedExperiment.rds:md5,778471a1436c249f1df5e1500c117470",
                 "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676",
                 "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe",
                 "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676",
@@ -1296,7 +1294,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.6"
         },
-        "timestamp": "2025-05-02T17:23:03.561712424"
+        "timestamp": "2025-05-02T20:07:25.787433287"
     },
     "Params: --aligner star_rsem - stub": {
         "content": [
diff --git a/tests/umi.nf.test.snap b/tests/umi.nf.test.snap
@@ -1364,8 +1364,6 @@
                 "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
                 "cmd_info.json:md5,809380ddce725a8fab75dd7741b64bf6",
                 "lib_format_counts.json:md5,d231ba7624b67eb654989f69530e2925",
-                "all_samples_gene.SummarizedExperiment.rds:md5,c9f3fb99bb418123d97931fc69c07bd5",
-                "all_samples_transcript.SummarizedExperiment.rds:md5,d00f0f57f399fcd4095572348ed80e2b",
                 "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676",
                 "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe",
                 "ambig_info.tsv:md5,0f0e3687e731243392685c550fb1d93f",
@@ -1509,7 +1507,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.6"
         },
-        "timestamp": "2025-05-02T17:41:34.57543678"
+        "timestamp": "2025-05-02T20:23:21.039706045"
     },
     "Params: --aligner hisat2 --umi_dedup_tool 'umicollapse'": {
         "content": [
@@ -2732,8 +2730,6 @@
                 "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
                 "cmd_info.json:md5,809380ddce725a8fab75dd7741b64bf6",
                 "lib_format_counts.json:md5,d231ba7624b67eb654989f69530e2925",
-                "all_samples_gene.SummarizedExperiment.rds:md5,492681cde948aab1bad52e8015b88c85",
-                "all_samples_transcript.SummarizedExperiment.rds:md5,e933f66abcb521faa61e39bf7555c142",
                 "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676",
                 "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe",
                 "RAP1_IAA_30M_REP1.umi_extract_1.fastq.gz:md5,e83d7f738fbbfaa541a2e71fe4663447",
@@ -2750,7 +2746,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.6"
         },
-        "timestamp": "2025-05-02T17:31:03.791729809"
+        "timestamp": "2025-05-02T20:13:02.972465499"
     },
     "--umi_dedup_tool 'umitools - stub": {
         "content": [

Original file line number	Diff line number	Diff line change
`@@ -1336,8 +1336,6 @@`
`1336`	`1336`	`"observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",`
`1337`	`1337`	`"cmd_info.json:md5,fe66c9d876645b9260d8c2488157d4d4",`
`1338`	`1338`	`"lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400",`
`1339`		`- "all_samples_gene.SummarizedExperiment.rds:md5,b888784394518aeb1658ed87ac75b0aa",`
`1340`		`- "all_samples_transcript.SummarizedExperiment.rds:md5,c2547a0f0e65ed6339c38f5d9f9a6753",`
`1341`	`1339`	`"R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676",`
`1342`	`1340`	`"tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe"`
`1343`	`1341`	`]`
`@@ -1346,6 +1344,6 @@`
`1346`	`1344`	`"nf-test": "0.9.2",`
`1347`	`1345`	`"nextflow": "24.10.6"`
`1348`	`1346`	`},`
`1349`		`- "timestamp": "2025-05-02T16:16:11.524273892"`
	`1347`	`+ "timestamp": "2025-05-02T18:55:20.186245374"`
`1350`	`1348`	`}`
`1351`	`1349`	`}`
Original file line number	Diff line number	Diff line change
`@@ -417,8 +417,6 @@`
`417`	`417`	`"observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",`
`418`	`418`	`"cmd_info.json:md5,3e6d06d032abd3f5cd7e79df1b5bcde0",`
`419`	`419`	`"lib_format_counts.json:md5,fce2c4840048c294c016f45f0df15384",`
`420`		`- "all_samples_gene.SummarizedExperiment.rds:md5,9374be23b333ce1cd865e7baf3d3c9cc",`
`421`		`- "all_samples_transcript.SummarizedExperiment.rds:md5,5887511793e75ecd158e295a66e001d6",`
`422`	`420`	`"R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676",`
`423`	`421`	`"tx2gene.tsv:md5,1be389a28cc26d94b19ea918959ac72e"`
`424`	`422`	`]`
`@@ -427,6 +425,6 @@`
`427`	`425`	`"nf-test": "0.9.2",`
`428`	`426`	`"nextflow": "24.10.6"`
`429`	`427`	`},`
`430`		`- "timestamp": "2025-05-02T16:34:02.48152685"`
	`428`	`+ "timestamp": "2025-05-02T19:16:45.468836741"`
`431`	`429`	`}`
`432`	`430`	`}`