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atrigilaatrigila
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use formula directly and update snapshot
1 parent 14ef874 commit 6248c6c

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2 files changed

+37
-39
lines changed

2 files changed

+37
-39
lines changed

‎modules/nf-core/deseq2/differential/templates/deseq2_differential.R‎

Lines changed: 1 addition & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -351,9 +351,7 @@ if ((is_valid_string(opt\$exclude_samples_col)) && (is_valid_string(opt\$exclude
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if (is_valid_string(opt\$formula)) {
353353
message("Using user-specified formula: ", opt\$formula)
354-
user_f <- as.formula(opt\$formula)
355-
model_f <- update(user_f, ~ 0 + .)
356-
model <- paste(as.character(model_f), collapse = " ")
354+
model <- opt\$formula
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} else {
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model <- '~ 0'
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‎modules/nf-core/deseq2/differential/tests/main.nf.test.snap‎

Lines changed: 36 additions & 36 deletions
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,7 @@
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"formula": "~ genotype * treatment",
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"comparison": "genotypeWT.treatmentTreated"
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},
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"genotype_WT_KO_treatment_Control_Treated.deseq2.results.tsv:md5,793d90d52dcaa7948be0714a7f2f565d"
11+
"genotype_WT_KO_treatment_Control_Treated.deseq2.results.tsv:md5,5612fc7e92a7a9b497b9198471ed3602"
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]
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],
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[
@@ -51,7 +51,7 @@
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"formula": "~ genotype * treatment",
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"comparison": "genotypeWT.treatmentTreated"
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},
54-
"genotype_WT_KO_treatment_Control_Treated.deseq2.model.txt:md5,1ccfae04123ff7797317d5bbd9080f00"
54+
"genotype_WT_KO_treatment_Control_Treated.deseq2.model.txt:md5,82165b8b24da8f8cffafa457290feeb3"
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]
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],
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[
@@ -61,11 +61,11 @@
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"genotype_WT_KO_treatment_Control_Treated.deseq2.dispersion.pdf",
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"genotype_WT_KO_treatment_Control_Treated.dds.rld.rds"
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],
64+
"timestamp": "2026-03-26T21:10:41.865554487",
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"meta": {
65-
"nf-test": "0.9.3",
66-
"nextflow": "25.04.2"
67-
},
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"timestamp": "2026-01-20T14:49:04.573809688"
66+
"nf-test": "0.9.5",
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"nextflow": "25.10.4"
68+
}
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},
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"mouse - contrasts - matrix": {
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"content": [
@@ -190,11 +190,11 @@
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"treatment_mCherry_hND6_.deseq2.dispersion.pdf",
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"treatment_mCherry_hND6_.dds.rld.rds"
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],
193+
"timestamp": "2026-01-20T14:54:20.534669297",
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.04.2"
196-
},
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"timestamp": "2026-01-20T14:54:20.534669297"
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}
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},
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"mouse - contrasts - matrix - exclude samples": {
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"content": [
@@ -319,11 +319,11 @@
319319
"treatment_mCherry_hND6_.deseq2.dispersion.pdf",
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"treatment_mCherry_hND6_.dds.rld.rds"
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],
322+
"timestamp": "2026-01-20T14:57:07.846675354",
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.04.2"
325-
},
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"timestamp": "2026-01-20T14:57:07.846675354"
326+
}
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},
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"mouse - contrasts - matrix - lengths": {
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"content": [
@@ -448,11 +448,11 @@
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"treatment_mCherry_hND6_.deseq2.dispersion.pdf",
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"treatment_mCherry_hND6_.dds.rld.rds"
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],
451+
"timestamp": "2026-01-20T14:54:41.568608327",
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"meta": {
452453
"nf-test": "0.9.3",
453454
"nextflow": "25.04.2"
454-
},
455-
"timestamp": "2026-01-20T14:54:41.568608327"
455+
}
456456
},
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"mouse - contrasts - matrix - strip spikes": {
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"content": [
@@ -577,11 +577,11 @@
577577
"treatment_mCherry_hND6_.deseq2.dispersion.pdf",
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"treatment_mCherry_hND6_.dds.rld.rds"
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],
580+
"timestamp": "2026-01-20T14:55:44.78705434",
580581
"meta": {
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"nf-test": "0.9.3",
582583
"nextflow": "25.04.2"
583-
},
584-
"timestamp": "2026-01-20T14:55:44.78705434"
584+
}
585585
},
586586
"RNAseq - Feature Counts - formula + limma contrast string - interaction": {
587587
"content": [
@@ -635,7 +635,7 @@
635635
"formula": "~ 0 + genotype",
636636
"comparison": "genotypeWT - genotypeKO"
637637
},
638-
"genotype_WT_KO.deseq2.model.txt:md5,ac7205ad2d20dc34aedba90032d06629"
638+
"genotype_WT_KO.deseq2.model.txt:md5,227c742304821b46168b1ebf10adfdce"
639639
]
640640
],
641641
[
@@ -645,11 +645,11 @@
645645
"genotype_WT_KO.deseq2.dispersion.pdf",
646646
"genotype_WT_KO.dds.rld.rds"
647647
],
648+
"timestamp": "2026-03-26T21:15:08.277275511",
648649
"meta": {
649-
"nf-test": "0.9.3",
650-
"nextflow": "25.04.2"
651-
},
652-
"timestamp": "2026-01-20T14:51:57.150384623"
650+
"nf-test": "0.9.5",
651+
"nextflow": "25.10.4"
652+
}
653653
},
654654
"mouse - contrasts - matrix - csv": {
655655
"content": [
@@ -723,11 +723,11 @@
723723
"treatment_mCherry_hND6_.deseq2.dispersion.pdf",
724724
"treatment_mCherry_hND6_.dds.rld.rds"
725725
],
726+
"timestamp": "2026-01-20T14:56:05.923791453",
726727
"meta": {
727728
"nf-test": "0.9.3",
728729
"nextflow": "25.04.2"
729-
},
730-
"timestamp": "2026-01-20T14:56:05.923791453"
730+
}
731731
},
732732
"mouse - contrasts - matrix - no blocking": {
733733
"content": [
@@ -852,11 +852,11 @@
852852
"treatment_mCherry_hND6_.deseq2.dispersion.pdf",
853853
"treatment_mCherry_hND6_.dds.rld.rds"
854854
],
855+
"timestamp": "2026-01-20T14:55:02.666674563",
855856
"meta": {
856857
"nf-test": "0.9.3",
857858
"nextflow": "25.04.2"
858-
},
859-
"timestamp": "2026-01-20T14:55:02.666674563"
859+
}
860860
},
861861
"RNAseq - Feature Counts - formula + limma contrast string - shrunken": {
862862
"content": [
@@ -910,7 +910,7 @@
910910
"formula": "~ 0 + genotype",
911911
"comparison": "genotypeWT - genotypeKO"
912912
},
913-
"genotype_WT_KO.deseq2.model.txt:md5,ac7205ad2d20dc34aedba90032d06629"
913+
"genotype_WT_KO.deseq2.model.txt:md5,227c742304821b46168b1ebf10adfdce"
914914
]
915915
],
916916
[
@@ -920,11 +920,11 @@
920920
"genotype_WT_KO.deseq2.dispersion.pdf",
921921
"genotype_WT_KO.dds.rld.rds"
922922
],
923+
"timestamp": "2026-03-26T21:19:23.811021031",
923924
"meta": {
924-
"nf-test": "0.9.3",
925-
"nextflow": "25.04.2"
926-
},
927-
"timestamp": "2026-01-20T14:53:58.660220114"
925+
"nf-test": "0.9.5",
926+
"nextflow": "25.10.4"
927+
}
928928
},
929929
"mouse - contrasts - matrix - subset to contrast": {
930930
"content": [
@@ -1049,11 +1049,11 @@
10491049
"treatment_mCherry_hND6_.deseq2.dispersion.pdf",
10501050
"treatment_mCherry_hND6_.dds.rld.rds"
10511051
],
1052+
"timestamp": "2026-01-20T14:56:47.562017144",
10521053
"meta": {
10531054
"nf-test": "0.9.3",
10541055
"nextflow": "25.04.2"
1055-
},
1056-
"timestamp": "2026-01-20T14:56:47.562017144"
1056+
}
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},
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"mouse - contrasts - matrix - spikes": {
10591059
"content": [
@@ -1178,11 +1178,11 @@
11781178
"treatment_mCherry_hND6_.deseq2.dispersion.pdf",
11791179
"treatment_mCherry_hND6_.dds.rld.rds"
11801180
],
1181+
"timestamp": "2026-01-20T14:55:23.654595481",
11811182
"meta": {
11821183
"nf-test": "0.9.3",
11831184
"nextflow": "25.04.2"
1184-
},
1185-
"timestamp": "2026-01-20T14:55:23.654595481"
1185+
}
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},
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"mouse - contrasts - matrix - vst nsub": {
11881188
"content": [
@@ -1307,11 +1307,11 @@
13071307
"treatment_mCherry_hND6_.deseq2.dispersion.pdf",
13081308
"treatment_mCherry_hND6_.dds.rld.rds"
13091309
],
1310+
"timestamp": "2026-01-20T14:56:26.669994057",
13101311
"meta": {
13111312
"nf-test": "0.9.3",
13121313
"nextflow": "25.04.2"
1313-
},
1314-
"timestamp": "2026-01-20T14:56:26.669994057"
1314+
}
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},
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"mouse - contrasts - matrix - stub": {
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"content": [
@@ -1728,10 +1728,10 @@
17281728
]
17291729
}
17301730
],
1731+
"timestamp": "2026-01-20T14:57:21.703291049",
17311732
"meta": {
17321733
"nf-test": "0.9.3",
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"nextflow": "25.04.2"
1734-
},
1735-
"timestamp": "2026-01-20T14:57:21.703291049"
1735+
}
17361736
}
17371737
}

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