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use formula directly without intercept in deseq2 #11062

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use formula directly without intercept in deseq2 #11062

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4 changes: 1 addition & 3 deletions modules/nf-core/deseq2/differential/templates/deseq2_differential.R
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Original file line number Diff line number Diff line change
Expand Up @@ -351,9 +351,7 @@ if ((is_valid_string(opt\$exclude_samples_col)) && (is_valid_string(opt\$exclude

if (is_valid_string(opt\$formula)) {
message("Using user-specified formula: ", opt\$formula)
user_f <- as.formula(opt\$formula)
model_f <- update(user_f, ~ 0 + .)
model <- paste(as.character(model_f), collapse = " ")
model <- opt\$formula
} else {
model <- '~ 0'

Expand Down
72 changes: 36 additions & 36 deletions modules/nf-core/deseq2/differential/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@
"formula": "~ genotype * treatment",
"comparison": "genotypeWT.treatmentTreated"
},
"genotype_WT_KO_treatment_Control_Treated.deseq2.results.tsv:md5,793d90d52dcaa7948be0714a7f2f565d"
"genotype_WT_KO_treatment_Control_Treated.deseq2.results.tsv:md5,5612fc7e92a7a9b497b9198471ed3602"
]
],
[
Expand Down Expand Up @@ -51,7 +51,7 @@
"formula": "~ genotype * treatment",
"comparison": "genotypeWT.treatmentTreated"
},
"genotype_WT_KO_treatment_Control_Treated.deseq2.model.txt:md5,1ccfae04123ff7797317d5bbd9080f00"
"genotype_WT_KO_treatment_Control_Treated.deseq2.model.txt:md5,82165b8b24da8f8cffafa457290feeb3"
]
],
[
Expand All @@ -61,11 +61,11 @@
"genotype_WT_KO_treatment_Control_Treated.deseq2.dispersion.pdf",
"genotype_WT_KO_treatment_Control_Treated.dds.rld.rds"
],
"timestamp": "2026-03-26T21:10:41.865554487",
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.04.2"
},
"timestamp": "2026-01-20T14:49:04.573809688"
"nf-test": "0.9.5",
"nextflow": "25.10.4"
}
},
"mouse - contrasts - matrix": {
"content": [
Expand Down Expand Up @@ -190,11 +190,11 @@
"treatment_mCherry_hND6_.deseq2.dispersion.pdf",
"treatment_mCherry_hND6_.dds.rld.rds"
],
"timestamp": "2026-01-20T14:54:20.534669297",
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.04.2"
},
"timestamp": "2026-01-20T14:54:20.534669297"
}
},
"mouse - contrasts - matrix - exclude samples": {
"content": [
Expand Down Expand Up @@ -319,11 +319,11 @@
"treatment_mCherry_hND6_.deseq2.dispersion.pdf",
"treatment_mCherry_hND6_.dds.rld.rds"
],
"timestamp": "2026-01-20T14:57:07.846675354",
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.04.2"
},
"timestamp": "2026-01-20T14:57:07.846675354"
}
},
"mouse - contrasts - matrix - lengths": {
"content": [
Expand Down Expand Up @@ -448,11 +448,11 @@
"treatment_mCherry_hND6_.deseq2.dispersion.pdf",
"treatment_mCherry_hND6_.dds.rld.rds"
],
"timestamp": "2026-01-20T14:54:41.568608327",
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.04.2"
},
"timestamp": "2026-01-20T14:54:41.568608327"
}
},
"mouse - contrasts - matrix - strip spikes": {
"content": [
Expand Down Expand Up @@ -577,11 +577,11 @@
"treatment_mCherry_hND6_.deseq2.dispersion.pdf",
"treatment_mCherry_hND6_.dds.rld.rds"
],
"timestamp": "2026-01-20T14:55:44.78705434",
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.04.2"
},
"timestamp": "2026-01-20T14:55:44.78705434"
}
},
"RNAseq - Feature Counts - formula + limma contrast string - interaction": {
"content": [
Expand Down Expand Up @@ -635,7 +635,7 @@
"formula": "~ 0 + genotype",
"comparison": "genotypeWT - genotypeKO"
},
"genotype_WT_KO.deseq2.model.txt:md5,ac7205ad2d20dc34aedba90032d06629"
"genotype_WT_KO.deseq2.model.txt:md5,227c742304821b46168b1ebf10adfdce"
]
],
[
Expand All @@ -645,11 +645,11 @@
"genotype_WT_KO.deseq2.dispersion.pdf",
"genotype_WT_KO.dds.rld.rds"
],
"timestamp": "2026-03-26T21:15:08.277275511",
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.04.2"
},
"timestamp": "2026-01-20T14:51:57.150384623"
"nf-test": "0.9.5",
"nextflow": "25.10.4"
}
},
"mouse - contrasts - matrix - csv": {
"content": [
Expand Down Expand Up @@ -723,11 +723,11 @@
"treatment_mCherry_hND6_.deseq2.dispersion.pdf",
"treatment_mCherry_hND6_.dds.rld.rds"
],
"timestamp": "2026-01-20T14:56:05.923791453",
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.04.2"
},
"timestamp": "2026-01-20T14:56:05.923791453"
}
},
"mouse - contrasts - matrix - no blocking": {
"content": [
Expand Down Expand Up @@ -852,11 +852,11 @@
"treatment_mCherry_hND6_.deseq2.dispersion.pdf",
"treatment_mCherry_hND6_.dds.rld.rds"
],
"timestamp": "2026-01-20T14:55:02.666674563",
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.04.2"
},
"timestamp": "2026-01-20T14:55:02.666674563"
}
},
"RNAseq - Feature Counts - formula + limma contrast string - shrunken": {
"content": [
Expand Down Expand Up @@ -910,7 +910,7 @@
"formula": "~ 0 + genotype",
"comparison": "genotypeWT - genotypeKO"
},
"genotype_WT_KO.deseq2.model.txt:md5,ac7205ad2d20dc34aedba90032d06629"
"genotype_WT_KO.deseq2.model.txt:md5,227c742304821b46168b1ebf10adfdce"
]
],
[
Expand All @@ -920,11 +920,11 @@
"genotype_WT_KO.deseq2.dispersion.pdf",
"genotype_WT_KO.dds.rld.rds"
],
"timestamp": "2026-03-26T21:19:23.811021031",
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.04.2"
},
"timestamp": "2026-01-20T14:53:58.660220114"
"nf-test": "0.9.5",
"nextflow": "25.10.4"
}
},
"mouse - contrasts - matrix - subset to contrast": {
"content": [
Expand Down Expand Up @@ -1049,11 +1049,11 @@
"treatment_mCherry_hND6_.deseq2.dispersion.pdf",
"treatment_mCherry_hND6_.dds.rld.rds"
],
"timestamp": "2026-01-20T14:56:47.562017144",
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.04.2"
},
"timestamp": "2026-01-20T14:56:47.562017144"
}
},
"mouse - contrasts - matrix - spikes": {
"content": [
Expand Down Expand Up @@ -1178,11 +1178,11 @@
"treatment_mCherry_hND6_.deseq2.dispersion.pdf",
"treatment_mCherry_hND6_.dds.rld.rds"
],
"timestamp": "2026-01-20T14:55:23.654595481",
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.04.2"
},
"timestamp": "2026-01-20T14:55:23.654595481"
}
},
"mouse - contrasts - matrix - vst nsub": {
"content": [
Expand Down Expand Up @@ -1307,11 +1307,11 @@
"treatment_mCherry_hND6_.deseq2.dispersion.pdf",
"treatment_mCherry_hND6_.dds.rld.rds"
],
"timestamp": "2026-01-20T14:56:26.669994057",
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.04.2"
},
"timestamp": "2026-01-20T14:56:26.669994057"
}
},
"mouse - contrasts - matrix - stub": {
"content": [
Expand Down Expand Up @@ -1728,10 +1728,10 @@
]
}
],
"timestamp": "2026-01-20T14:57:21.703291049",
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.04.2"
},
"timestamp": "2026-01-20T14:57:21.703291049"
}
}
}
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