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Merged
delfiterradas merged 15 commits into from
Dec 9, 2025
Merged

Fix dream to show more than 10 results #9507

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24ceeff
fix: dream to show more than 10 results
atrigila Dec 4, 2025
9014af7
test: update snapshots
atrigila Dec 4, 2025
907f541
test: update snapshots
atrigila Dec 4, 2025
f76c9f9
feat: add round digits option and update snapshots again
atrigila Dec 4, 2025
320a74f
Merge branch 'master' into fix_dream
atrigila Dec 4, 2025
a839d05
fix: improve code formatting and update test snapshots
atrigila Dec 4, 2025
49b412d
Merge branch 'fix_dream' of https://github.com/atrigila/modules into …
atrigila Dec 4, 2025
c31e99c
Fix tests and update snapshots
delfiterradas Dec 4, 2025
51baa3e
Update snapshot for `abundance_differential_filter` subworkflow
delfiterradas Dec 4, 2025
d7da556
Fix tests with unstable content
delfiterradas Dec 4, 2025
ce149b6
Fix unstable files in test for `abundance_differential_filter` subwor…
delfiterradas Dec 4, 2025
78471f1
Merge branch 'master' into fix_dream
atrigila Dec 5, 2025
d8d4b4d
Merge branch 'master' into fix_dream
atrigila Dec 7, 2025
aa562ff
Merge branch 'master' into fix_dream
delfiterradas Dec 9, 2025
12c4fde
Merge branch 'master' into fix_dream
delfiterradas Dec 9, 2025
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15 changes: 13 additions & 2 deletions modules/nf-core/variancepartition/dream/templates/dream.R
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Original file line number Diff line number Diff line change
Expand Up @@ -80,6 +80,7 @@ opt <- list(
winsor_tail_p = "0.05,0.1", # Winsor tail probabilities for eBayes
ddf = "adaptive", # 'Satterthwaite', 'Kenward-Roger', or 'adaptive'
reml = FALSE,
round_digits = NULL,
formula = "$formula", # User-specified formula (e.g. "~ + (1 | sample_number)")
apply_voom = FALSE # Whether to apply `voomWithDreamWeights`
)
Expand Down Expand Up @@ -107,6 +108,10 @@ opt\$p.value <- as.numeric(opt\$p.value)
opt\$lfc <- as.numeric(opt\$lfc)
opt\$confint <- as.logical(opt\$confint)

if (!is.null(opt\$round_digits)){
opt\$round_digits <- as.numeric(opt\$round_digits)
}

# Load metadata
metadata <- read_delim_flexible(opt\$sample_file, header = TRUE, stringsAsFactors = TRUE)
rownames(metadata) <- metadata[[opt\$sample_id_col]]
Expand Down Expand Up @@ -178,22 +183,28 @@ if (!is.null(opt\$contrast_string)) {
stdev.coef.lim = stdev_coef_lim_vals,
trend = opt\$trend, robust = opt\$robust,
winsor.tail.p = winsor_tail_p_vals)
results <- topTable(fit2,
results <- topTable(fit2, number = Inf,
adjust.method = opt\$adjust.method,
p.value = opt\$p.value, lfc = opt\$lfc, confint = opt\$confint)

} else {
coef_name <- paste0(opt\$contrast_variable, opt\$contrast_target)
cat("Using default contrast matrix:", coef_name, "\n")

results <- topTable(fitmm, coef = coef_name,
results <- topTable(fitmm, coef = coef_name, number = Inf,
adjust.method = opt\$adjust.method, p.value = opt\$p.value,
lfc = opt\$lfc, confint = opt\$confint)
}

results\$gene_id <- rownames(results)
results <- results[, c("gene_id", setdiff(names(results), "gene_id"))]

# Round results if required
if (!is.null(opt\$round_digits)) {
numeric_columns <- vapply(results, is.numeric, logical(1))
results[numeric_columns] <- lapply(results[numeric_columns], round, digits = opt\$round_digits)
}

# Export topTable results
write.table(results, file = paste(opt\$output_prefix, 'dream.results.tsv', sep = '.'),
col.names = TRUE, row.names = FALSE, sep = '\t', quote = FALSE )
Expand Down
47 changes: 35 additions & 12 deletions modules/nf-core/variancepartition/dream/tests/main.nf.test
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@ nextflow_process {

name "Test Process VARIANCEPARTITION_DREAM"
script "../main.nf"
config "./nextflow.config"
process "VARIANCEPARTITION_DREAM"

tag "modules"
Expand All @@ -12,6 +13,9 @@ nextflow_process {
test("RNAseq - Feature Counts - formula + comparison contrast string - interaction") {

when {
params {
module_args = "--round_digits 2"
}
process {
"""
input[0] = Channel.of([
Expand Down Expand Up @@ -40,8 +44,8 @@ nextflow_process {
assertAll(
{ assert process.success },
{ assert path(process.out.results[0][1]).getText().contains("gene_id\tlogFC\tAveExpr\tt\tP.Value\tadj.P.Val\tB") },
{ assert path(process.out.results[0][1]).getText().contains("0.8333") },
{ assert path(process.out.results[0][1]).getText().contains("13.5\t21.125\t4.40") },
{ assert path(process.out.results[0][1]).getText().contains("0.83") },
{ assert path(process.out.results[0][1]).getText().contains("13.5\t21.12\t4.41") },
{ assert snapshot(process.out.model, process.out.versions).match() }
)
}
Expand All @@ -50,6 +54,9 @@ nextflow_process {
test("Mus musculus - expression table - contrasts") {

when {
params {
module_args = "--round_digits 2"
}
process {
"""
input[0] = Channel.of(['id': 'treatment_mCherry_hND6', 'variable': 'treatment', 'reference': 'mCherry', 'target': 'hND6', 'blocking_factors':null, 'formula':null])
Expand Down Expand Up @@ -77,6 +84,9 @@ nextflow_process {
test("Mus musculus - expression table - contrasts + formula + comparison contrast string") {

when {
params {
module_args = "--round_digits 2"
}
process {
"""
input[0] = Channel.of(['id': 'treatment_mCherry_hND6', 'variable': 'treatment', 'reference': 'mCherry', 'target': 'hND6', 'blocking_factors':'sample_number', 'formula':'~ treatment', 'comparison':'treatmenthND6'])
Expand All @@ -98,16 +108,20 @@ nextflow_process {
assertAll(
{ assert process.success },
{ assert path(process.out.results[0][1]).getText().contains("gene_id\tlogFC\tAveExpr\tt\tP.Value\tadj.P.Val\tB") },
{ assert path(process.out.results[0][1]).getText().contains("849.6666") },
{ assert path(process.out.results[0][1]).getText().contains("1050\t549\t3.78") }
)
{ assert path(process.out.results[0][1]).getText().contains("849.67") },
{ assert path(process.out.results[0][1]).getText().contains("1050\t549\t3.78") },
{ assert snapshot(process.out.model, process.out.versions).match() }
)
}
}


test("Mus musculus - expression table - contrasts + formula + weighted comparison contrast string") {

when {
params {
module_args = "--round_digits 2"
}
process {
"""
input[0] = Channel.of(['id': 'treatment_mCherry_hND6', 'variable': 'treatment', 'reference': 'mCherry', 'target': 'hND6', 'blocking_factors':'sample_number', 'formula':'~ 0 + treatment', 'comparison':'2 * treatmenthND6 - treatmentmCherry'])
Expand All @@ -128,17 +142,20 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out.model, process.out.versions).match() },
{ assert path(process.out.results[0][1]).getText().contains("gene_id\tlogFC\tAveExpr\tt\tP.Value\tadj.P.Val\tB") },
{ assert path(process.out.results[0][1]).getText().contains("2124\t549\t4.83") },
{ assert path(process.out.results[0][1]).getText().contains("1707.33") }
)
{ assert path(process.out.results[0][1]).getText().contains("2124\t549\t4.84") },
{ assert path(process.out.results[0][1]).getText().contains("1707.33") },
{ assert snapshot(process.out.model, process.out.versions).match() }
)
}
}

test("Mus musculus - expression table - contrasts + formula + comparison contrast string - no intercept") {

when {
params {
module_args = "--round_digits 2"
}
process {
"""
input[0] = Channel.of(['id': 'treatment_mCherry_hND6', 'variable': 'treatment', 'reference': 'mCherry', 'target': 'hND6', 'blocking_factors':'sample_number', 'formula':'~ 0 + treatment + sample_number', 'comparison':'treatmenthND6 - treatmentmCherry'])
Expand All @@ -161,15 +178,18 @@ nextflow_process {
{ assert process.success },
{ assert snapshot(process.out.model, process.out.versions).match() },
{ assert path(process.out.results[0][1]).getText().contains("gene_id\tlogFC\tAveExpr\tt\tP.Value\tadj.P.Val\tB") },
{ assert path(process.out.results[0][1]).getText().contains("-95.6666") },
{ assert path(process.out.results[0][1]).getText().contains("1050\t549\t4.15") }
)
{ assert path(process.out.results[0][1]).getText().contains("-95.67") },
{ assert path(process.out.results[0][1]).getText().contains("1050\t549\t4.16") }
)
}
}

test("Mus musculus - expression table - contrasts + blocking factors") {

when {
params {
module_args = "--round_digits 2"
}
process {
"""
input[0] = Channel.of(['id': 'treatment_mCherry_hND6', 'variable': 'treatment', 'reference': 'mCherry', 'target': 'hND6', 'blocking_factors':'sample_number', 'formula':'~ treatment + (1 | sample_number)'])
Expand Down Expand Up @@ -199,6 +219,9 @@ nextflow_process {

options '-stub'
when {
params {
module_args = "--round_digits 2"
}
process {
"""
input[0] = Channel.of(['id': 'treatment_mCherry_hND6', 'variable': 'treatment', 'reference': 'mCherry', 'target': 'hND6', 'blocking_factors':'sample_number', 'formula':'~ treatment + (1 | sample_number)'])
Expand Down
113 changes: 33 additions & 80 deletions modules/nf-core/variancepartition/dream/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -20,10 +20,10 @@
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-11-10T16:15:40.192241719"
"timestamp": "2025-12-04T21:00:34.198143553"
},
"RNAseq - Feature Counts - formula + comparison contrast string - interaction": {
"content": [
Expand All @@ -46,10 +46,10 @@
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-11-10T16:14:20.039981065"
"timestamp": "2025-12-04T20:59:55.416875311"
},
"Mus musculus - expression table - contrasts + blocking factors": {
"content": [
Expand All @@ -64,7 +64,7 @@
"blocking_factors": "sample_number",
"formula": "~ treatment + (1 | sample_number)"
},
"treatment_mCherry_hND6.dream.results.tsv:md5,ad7e79a25bf407b210e3ebfbf734f68e"
"treatment_mCherry_hND6.dream.results.tsv:md5,df0717ddf702543c375c1a5f4eae3fd7"
]
],
"1": [
Expand Down Expand Up @@ -106,7 +106,7 @@
"blocking_factors": "sample_number",
"formula": "~ treatment + (1 | sample_number)"
},
"treatment_mCherry_hND6.dream.results.tsv:md5,ad7e79a25bf407b210e3ebfbf734f68e"
"treatment_mCherry_hND6.dream.results.tsv:md5,df0717ddf702543c375c1a5f4eae3fd7"
]
],
"versions": [
Expand All @@ -115,10 +115,10 @@
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-11-10T16:18:15.340812595"
"timestamp": "2025-12-04T19:20:24.632444115"
},
"Mus musculus - expression table - contrasts + blocking factors stub": {
"content": [
Expand Down Expand Up @@ -210,82 +210,35 @@
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-11-10T16:15:20.824781388"
"timestamp": "2025-12-04T21:02:12.893838766"
},
"Mus musculus - expression table - contrasts + formula + comparison contrast string": {
"content": [
{
"0": [
[
{
"id": "treatment_mCherry_hND6",
"variable": "treatment",
"reference": "mCherry",
"target": "hND6",
"blocking_factors": "sample_number",
"formula": "~ treatment",
"comparison": "treatmenthND6"
},
"treatment_mCherry_hND6.dream.results.tsv:md5,0b9521f3aafdbc7f2df761bdc8b1a1ea"
]
],
"1": [
[
{
"id": "treatment_mCherry_hND6",
"variable": "treatment",
"reference": "mCherry",
"target": "hND6",
"blocking_factors": "sample_number",
"formula": "~ treatment",
"comparison": "treatmenthND6"
},
"treatment_mCherry_hND6.dream.model.txt:md5,8cb944a29e3d3d0e540048b4d8331b17"
]
],
"2": [
"versions.yml:md5,fc1f26eb2194018e99fc2916332676b7"
],
"model": [
[
{
"id": "treatment_mCherry_hND6",
"variable": "treatment",
"reference": "mCherry",
"target": "hND6",
"blocking_factors": "sample_number",
"formula": "~ treatment",
"comparison": "treatmenthND6"
},
"treatment_mCherry_hND6.dream.model.txt:md5,8cb944a29e3d3d0e540048b4d8331b17"
]
],
"results": [
[
{
"id": "treatment_mCherry_hND6",
"variable": "treatment",
"reference": "mCherry",
"target": "hND6",
"blocking_factors": "sample_number",
"formula": "~ treatment",
"comparison": "treatmenthND6"
},
"treatment_mCherry_hND6.dream.results.tsv:md5,0b9521f3aafdbc7f2df761bdc8b1a1ea"
]
],
"versions": [
"versions.yml:md5,fc1f26eb2194018e99fc2916332676b7"
[
[
{
"id": "treatment_mCherry_hND6",
"variable": "treatment",
"reference": "mCherry",
"target": "hND6",
"blocking_factors": "sample_number",
"formula": "~ treatment",
"comparison": "treatmenthND6"
},
"treatment_mCherry_hND6.dream.model.txt:md5,8cb944a29e3d3d0e540048b4d8331b17"
]
}
],
[
"versions.yml:md5,fc1f26eb2194018e99fc2916332676b7"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-04-07T17:45:38.612858235"
"timestamp": "2025-12-04T21:02:02.754734146"
}
}
8 changes: 8 additions & 0 deletions subworkflows/nf-core/abundance_differential_filter/tests/dream.config
View file
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Original file line number Diff line number Diff line change
@@ -0,0 +1,8 @@
process {
withName: 'VARIANCEPARTITION_DREAM' {
ext.args = { [
"--round_digits 2"
].join(' ').trim() }
ext.prefix = { "${meta.id}_${meta.differential_method}" }
}
}
8 changes: 4 additions & 4 deletions subworkflows/nf-core/abundance_differential_filter/tests/main.nf.test
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@ nextflow_workflow {
tag "variancepartition/dream"

test("dream") {
config './dream.config'
tag "dream_simple"

when {
Expand Down Expand Up @@ -59,8 +60,8 @@ nextflow_workflow {
then {
assertAll(
{ assert workflow.success },
{ assert path(workflow.out.results_genewise[0][1]).getText().contains("gene_id\tlogFC\tAveExpr\tt\tP.Value\tadj.P.Val\tB") },
{ assert snapshot(
workflow.out.results_genewise,
workflow.out.results_genewise_filtered,
workflow.out.model,
workflow.out.versions
Expand All @@ -70,6 +71,7 @@ nextflow_workflow {
}

test("dream - complex contrast - literal contrast string comparison") {
config './dream.config'
tag "dream_complex"

when {
Expand Down Expand Up @@ -114,10 +116,8 @@ nextflow_workflow {
assertAll(
{ assert workflow.success },
{ assert path(workflow.out.results_genewise[0][1]).getText().contains("gene_id\tlogFC\tAveExpr\tt\tP.Value\tadj.P.Val\tB") },
{ assert path(workflow.out.results_genewise[0][1]).getText().contains("-95.6666") },
{ assert path(workflow.out.results_genewise[0][1]).getText().contains("1050\t549\t4.15") },
{ assert snapshot(
file(workflow.out.results_genewise[0][1]).name,
workflow.out.results_genewise_filtered,
workflow.out.model,
workflow.out.versions
).match() }
Expand Down
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