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Merged
atrigila merged 8 commits into from
Apr 2, 2025
Merged

Support formula in abundance_differential_filter and associated modules #8171

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a5708ca
refact: update structure of `variancepartition/dream`
atrigila Mar 31, 2025
9ed4bfd
refact: allow formula in channel inputs
atrigila Mar 31, 2025
eac4f3a
docs: add formula to meta
atrigila Mar 31, 2025
c1a080e
fix: unstable digits in limma modules
atrigila Mar 31, 2025
1b86fb8
Apply suggestions from code review
atrigila Apr 1, 2025
12d8303
refact: use formula in `variancepartition/dream` only
atrigila Apr 1, 2025
14f754d
docs: remove meta example
atrigila Apr 1, 2025
9c611ef
Merge branch 'master' into variancepartition_fix
atrigila Apr 2, 2025
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90 changes: 45 additions & 45 deletions modules/nf-core/deseq2/differential/tests/main.nf.test
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ nextflow_process {
test("mouse - contrasts - matrix") {

config './contrasts_matrix.config'

when {
process {
"""
Expand All @@ -24,13 +24,13 @@ nextflow_process {
tuple(it, it.variable, it.reference, it.target)
}
ch_matrix = [
[id: 'test'],
[id: 'test'],
file(expression_test_data_dir + 'SRP254919.samplesheet.csv', checkIfExists: true),
file(expression_test_data_dir + 'SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)
]
ch_spikes = [[],[]]
ch_lengths = [[],[]]

input[0] = ch_contrasts
input[1] = ch_matrix
input[2] = ch_spikes
Expand All @@ -52,7 +52,7 @@ nextflow_process {
file(process.out.dispersion_plot[0][1]).name,
file(process.out.rdata[0][1]).name
).match() },
{ assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
{ assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
)
}
}
Expand All @@ -72,15 +72,15 @@ nextflow_process {
tuple(it, it.variable, it.reference, it.target)
}
ch_matrix = [
[id: 'test'],
[id: 'test'],
file(expression_test_data_dir + 'SRP254919.samplesheet.csv', checkIfExists: true),
file(expression_test_data_dir + 'SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)
]
ch_lengths = [
[id: 'test'],
[id: 'test'],
file(expression_test_data_dir + 'SRP254919.spoofed_lengths.tsv', checkIfExists: true)
]

ch_spikes = [[],[]]

input[0] = ch_contrasts
Expand All @@ -105,7 +105,7 @@ nextflow_process {
file(process.out.dispersion_plot[0][1]).name,
file(process.out.rdata[0][1]).name
).match() },
{ assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
{ assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
)
}

Expand All @@ -114,7 +114,7 @@ nextflow_process {
test("mouse - contrasts - matrix - no blocking") {

config './contrasts_matrix_noblocking.config'

when {
process {
"""
Expand All @@ -126,13 +126,13 @@ nextflow_process {
tuple(it, it.variable, it.reference, it.target)
}
ch_matrix = [
[id: 'test'],
[id: 'test'],
file(expression_test_data_dir + 'SRP254919.samplesheet.csv', checkIfExists: true),
file(expression_test_data_dir + 'SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)
]
ch_spikes = [[],[]]
ch_lengths = [[],[]]

input[0] = ch_contrasts
input[1] = ch_matrix
input[2] = ch_spikes
Expand All @@ -154,15 +154,15 @@ nextflow_process {
file(process.out.dispersion_plot[0][1]).name,
file(process.out.rdata[0][1]).name
).match() },
{ assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
{ assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
)
}
}

test("mouse - contrasts - matrix - spikes") {

config './contrasts_matrix_spikes.config'

when {
process {
"""
Expand All @@ -174,16 +174,16 @@ nextflow_process {
tuple(it, it.variable, it.reference, it.target)
}
ch_matrix = [
[id: 'test'],
[id: 'test'],
file(expression_test_data_dir + 'SRP254919.samplesheet.csv', checkIfExists: true),
file(expression_test_data_dir + 'SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)
]
ch_spikes = [
['id':'ERCC'],
['id':'ERCC'],
file(expression_test_data_dir + 'SRP254919.spikes.tsv', checkIfExists: true)
]
ch_lengths = [[],[]]

input[0] = ch_contrasts
input[1] = ch_matrix
input[2] = ch_spikes
Expand All @@ -205,15 +205,15 @@ nextflow_process {
file(process.out.dispersion_plot[0][1]).name,
file(process.out.rdata[0][1]).name
).match() },
{ assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
{ assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
)
}
}

test("mouse - contrasts - matrix - strip spikes") {

config './contrasts_matrix.config'

when {
process {
"""
Expand All @@ -225,16 +225,16 @@ nextflow_process {
tuple(it, it.variable, it.reference, it.target)
}
ch_matrix = [
[id: 'test'],
[id: 'test'],
file(expression_test_data_dir + 'SRP254919.samplesheet.csv', checkIfExists: true),
file(expression_test_data_dir + 'SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)
]
ch_spikes = [
['id':'ERCC'],
['id':'ERCC'],
file(expression_test_data_dir + 'SRP254919.spikes.tsv', checkIfExists: true)
]
ch_lengths = [[],[]]

input[0] = ch_contrasts
input[1] = ch_matrix
input[2] = ch_spikes
Expand All @@ -256,15 +256,15 @@ nextflow_process {
file(process.out.dispersion_plot[0][1]).name,
file(process.out.rdata[0][1]).name
).match() },
{ assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
{ assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
)
}
}

test("mouse - contrasts - matrix - csv") {

config './contrasts_matrix.config'

when {
process {
"""
Expand All @@ -288,7 +288,7 @@ nextflow_process {
}
ch_spikes = [[],[]]
ch_lengths = [[],[]]

input[0] = ch_contrasts
input[1] = ch_matrix
input[2] = ch_spikes
Expand All @@ -310,15 +310,15 @@ nextflow_process {
file(process.out.dispersion_plot[0][1]).name,
file(process.out.rdata[0][1]).name
).match() },
{ assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
{ assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
)
}
}

test("mouse - contrasts - matrix - vst nsub") {

config './contrasts_matrix_vst_nsub.config'

when {
process {
"""
Expand All @@ -330,13 +330,13 @@ nextflow_process {
tuple(it, it.variable, it.reference, it.target)
}
ch_matrix = [
[id: 'test'],
[id: 'test'],
file(expression_test_data_dir + 'SRP254919.samplesheet.csv', checkIfExists: true),
file(expression_test_data_dir + 'SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)
]
ch_spikes = [[],[]]
ch_lengths = [[],[]]

input[0] = ch_contrasts
input[1] = ch_matrix
input[2] = ch_spikes
Expand All @@ -358,15 +358,15 @@ nextflow_process {
file(process.out.dispersion_plot[0][1]).name,
file(process.out.rdata[0][1]).name
).match() },
{ assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
{ assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
)
}
}

test("mouse - contrasts - matrix - subset to contrast") {

config './contrasts_matrix_subset_to_contrast.config'

when {
process {
"""
Expand All @@ -378,13 +378,13 @@ nextflow_process {
tuple(it, it.variable, it.reference, it.target)
}
ch_matrix = [
[id: 'test'],
[id: 'test'],
file(expression_test_data_dir + 'SRP254919.samplesheet.csv', checkIfExists: true),
file(expression_test_data_dir + 'SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)
]
ch_spikes = [[],[]]
ch_lengths = [[],[]]

input[0] = ch_contrasts
input[1] = ch_matrix
input[2] = ch_spikes
Expand All @@ -406,15 +406,15 @@ nextflow_process {
file(process.out.dispersion_plot[0][1]).name,
file(process.out.rdata[0][1]).name
).match() },
{ assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
{ assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
)
}
}

test("mouse - contrasts - matrix - exclude samples") {

config './contrasts_matrix_exclude_samples.config'

when {
process {
"""
Expand All @@ -426,13 +426,13 @@ nextflow_process {
tuple(it, it.variable, it.reference, it.target)
}
ch_matrix = [
[id: 'test'],
[id: 'test'],
file(expression_test_data_dir + 'SRP254919.samplesheet.csv', checkIfExists: true),
file(expression_test_data_dir + 'SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)
]
ch_spikes = [[],[]]
ch_lengths = [[],[]]

input[0] = ch_contrasts
input[1] = ch_matrix
input[2] = ch_spikes
Expand All @@ -454,16 +454,16 @@ nextflow_process {
file(process.out.dispersion_plot[0][1]).name,
file(process.out.rdata[0][1]).name
).match() },
{ assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
{ assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
)
}
}
test("mouse - contrasts - matrix - stub") {

config './contrasts_matrix.config'

options "-stub"

when {
process {
"""
Expand All @@ -475,13 +475,13 @@ nextflow_process {
tuple(it, it.variable, it.reference, it.target)
}
ch_matrix = [
[id: 'test'],
[id: 'test'],
file(expression_test_data_dir + 'SRP254919.samplesheet.csv', checkIfExists: true),
file(expression_test_data_dir + 'SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)
]
ch_spikes = [[],[]]
ch_lengths = [[],[]]

input[0] = ch_contrasts
input[1] = ch_matrix
input[2] = ch_spikes
Expand Down
6 changes: 3 additions & 3 deletions modules/nf-core/limma/differential/tests/main.nf.test
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -220,7 +220,7 @@ nextflow_process {
{ assert process.success },
{ assert snapshot(process.out.model, process.out.versions).match() },
{ assert path(process.out.results[0][1]).getText().contains("ENSMUSG00000023978\t-4.89014922224241") },
{ assert path(process.out.results[0][1]).getText().contains("ENSMUSG00000059991\t0.779227180297504") },
{ assert path(process.out.results[0][1]).getText().contains("ENSMUSG00000059991\t0.77922") },
{ assert path(process.out.normalised_counts[0][1]).getText().contains("ENSMUSG00000023978\t6.11247620232167") },
{ assert path(process.out.normalised_counts[0][1]).getText().contains("ENSMUSG00000059991\t4.52751370160052") }
)
Expand Down Expand Up @@ -249,7 +249,7 @@ nextflow_process {
{ assert process.success },
{ assert snapshot(process.out.model, process.out.versions).match() },
{ assert path(process.out.results[0][1]).getText().contains("ENSMUSG00000023978\t-2.84055986312942") },
{ assert path(process.out.results[0][1]).getText().contains("ENSMUSG00000059991\t0.705508451587681") },
{ assert path(process.out.results[0][1]).getText().contains("ENSMUSG00000059991\t0.7055") },
{ assert path(process.out.normalised_counts[0][1]).getText().contains("ENSMUSG00000023978\t6.11247620232167") },
{ assert path(process.out.normalised_counts[0][1]).getText().contains("ENSMUSG00000059991\t4.52751370160052") }
)
Expand Down Expand Up @@ -278,7 +278,7 @@ nextflow_process {
{ assert process.success },
{ assert snapshot(process.out.model, process.out.versions).match() },
{ assert path(process.out.results[0][1]).getText().contains("ENSMUSG00000023978\t-2.8363444336503") },
{ assert path(process.out.results[0][1]).getText().contains("ENSMUSG00000059991\t0.736009837885068") },
{ assert path(process.out.results[0][1]).getText().contains("ENSMUSG00000059991\t0.7360") },
{ assert path(process.out.normalised_counts[0][1]).getText().contains("ENSMUSG00000023978\t6.11247620232167") },
{ assert path(process.out.normalised_counts[0][1]).getText().contains("ENSMUSG00000059991\t4.52751370160052") }
)
Expand Down
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