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Enable complex contrast strings in DESeq2 (#9473)
* Enable complex contrast strings * Update docker image * Add test case with limma contrast string * Format changes and add test with shrinkage
1 parent c984ada commit d09b58a

6 files changed

Lines changed: 357 additions & 112 deletions

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‎modules/nf-core/deseq2/differential/environment.yml‎

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@@ -5,3 +5,4 @@ channels:
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- bioconda
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dependencies:
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- bioconda::bioconductor-deseq2=1.34.0
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- bioconda::bioconductor-limma=3.50.0

‎modules/nf-core/deseq2/differential/main.nf‎

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@@ -4,8 +4,8 @@ process DESEQ2_DIFFERENTIAL {
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conda "${moduleDir}/environment.yml"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bioconductor-deseq2:1.34.0--r41hc247a5b_3' :
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'biocontainers/bioconductor-deseq2:1.34.0--r41hc247a5b_3' }"
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'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a1/a15f5d61792b60b6179afd885db27d3fe60eb4c42e805c8887ed0416d88cb484/data' :
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'community.wave.seqera.io/library/bioconductor-deseq2_bioconductor-limma:b56a0c9ddc3e87e1' }"
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input:
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tuple val(meta), val(contrast_variable), val(reference), val(target), val(formula), val(comparison)

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

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@@ -231,6 +231,7 @@ for (file_input in c('count_file', 'sample_file')){
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library(DESeq2)
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library(BiocParallel)
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library(limma)
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################################################
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################################################
@@ -425,17 +426,25 @@ dds <- DESeq(
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if (!is.null(opt\$contrast_string)) {
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coef_names <- resultsNames(dds)
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if (!(opt\$contrast_string %in% coef_names)) {
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stop(sprintf(
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"Contrast '%s' not in design. Available coefficients: %s",
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opt\$contrast_string,
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paste(coef_names, collapse = ", ")
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))
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}
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if (opt\$contrast_string %in% coef_names) {
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# Direct coefficient name
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comp.results <- run_results(name = opt\$contrast_string)
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if (opt\$shrink_lfc) {
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comp.results <- run_shrink(coef = opt\$contrast_string)
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}
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} else {
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# Parse as limma-style contrast expression
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design_mat <- model.matrix(as.formula(model), data = as.data.frame(colData(dds)))
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colnames(design_mat) <- make.names(colnames(design_mat))
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numeric_contrast <- as.numeric(
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limma::makeContrasts(contrasts = opt\$contrast_string, levels = colnames(design_mat))
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)
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comp.results <- run_results(name = opt\$contrast_string)
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if (opt\$shrink_lfc) {
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comp.results <- run_shrink(coef = opt\$contrast_string)
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# Run DESeq2 results with numeric contrast
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comp.results <- run_results(contrast = numeric_contrast)
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if (opt\$shrink_lfc) {
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comp.results <- run_shrink(contrast = numeric_contrast)
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}
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}
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} else {
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contrast_var_tg_ref <- c(contrast_variable,
@@ -452,7 +461,7 @@ if (!is.null(opt\$contrast_string)) {
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if (!is.null(opt\$transcript_lengths_file)){
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size_factors = estimateSizeFactorsForMatrix(counts(dds) / assays(dds)[["avgTxLength"]])
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}else {
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} else {
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size_factors = sizeFactors(dds)
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}
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‎modules/nf-core/deseq2/differential/tests/contrasts_shrink.config‎

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@@ -0,0 +1,5 @@
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process {
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withName: 'DESEQ2_DIFFERENTIAL' {
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ext.args = { "--round_digits 2 --sample_id_col sample --vs_method rlog --shrink_lfc TRUE --seed 1" }
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}
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}

‎modules/nf-core/deseq2/differential/tests/main.nf.test‎

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@@ -57,6 +57,102 @@ nextflow_process {
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}
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}
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test("RNAseq - Feature Counts - formula + limma contrast string - interaction") {
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config './contrasts_interaction.config'
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when {
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process {
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"""
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input[0] = Channel.of([
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'id': 'genotype_WT_KO',
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'formula': '~ 0 + genotype',
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'comparison': 'genotypeWT - genotypeKO'
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])
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.map {
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tuple(it, it.variable, it.reference, it.target, it.formula, it.comparison)
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}
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input[1] = Channel.of([
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[ id: 'test' ],
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file("https://github.com/nf-core/test-datasets/raw/differentialabundance/modules_testdata/variancepartition_dream/metadata.tsv", checkIfExists: true),
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file("https://github.com/nf-core/test-datasets/raw/differentialabundance/modules_testdata/variancepartition_dream/counts.tsv", checkIfExists: true)
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])
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ch_spikes = [[],[]]
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ch_lengths = [[],[]]
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input[2] = ch_spikes
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input[3] = ch_lengths
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert snapshot(
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process.out.results,
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process.out.size_factors,
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process.out.normalised_counts,
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process.out.rlog_counts,
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process.out.vst_counts,
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process.out.model,
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process.out.versions,
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file(process.out.dispersion_plot[0][1]).name,
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file(process.out.rdata[0][1]).name
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).match() },
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{ assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
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)
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}
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}
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test("RNAseq - Feature Counts - formula + limma contrast string - shrunken") {
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config './contrasts_shrink.config'
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when {
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process {
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"""
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input[0] = Channel.of([
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'id': 'genotype_WT_KO',
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'formula': '~ 0 + genotype',
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'comparison': 'genotypeWT - genotypeKO'
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])
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.map {
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tuple(it, it.variable, it.reference, it.target, it.formula, it.comparison)
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}
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input[1] = Channel.of([
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[ id: 'test' ],
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file("https://github.com/nf-core/test-datasets/raw/differentialabundance/modules_testdata/variancepartition_dream/metadata.tsv", checkIfExists: true),
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file("https://github.com/nf-core/test-datasets/raw/differentialabundance/modules_testdata/variancepartition_dream/counts.tsv", checkIfExists: true)
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])
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ch_spikes = [[],[]]
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ch_lengths = [[],[]]
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input[2] = ch_spikes
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input[3] = ch_lengths
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert snapshot(
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process.out.results,
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process.out.size_factors,
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process.out.normalised_counts,
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process.out.rlog_counts,
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process.out.vst_counts,
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process.out.model,
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process.out.versions,
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file(process.out.dispersion_plot[0][1]).name,
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file(process.out.rdata[0][1]).name
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).match() },
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{ assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
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)
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}
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}
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test("mouse - contrasts - matrix") {
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config './contrasts_matrix.config'

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