diff --git a/modules.json b/modules.json index d42ec9eb..545d26d5 100644 --- a/modules.json +++ b/modules.json @@ -32,7 +32,7 @@ }, "deseq2/differential": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "9326d73af3fbe2ee90d9ce0a737461a727c5118e", "installed_by": ["modules"] }, "geoquery/getgeo": { diff --git a/modules/nf-core/deseq2/differential/environment.yml b/modules/nf-core/deseq2/differential/environment.yml index 4f0b1d10..0ab1d0b6 100644 --- a/modules/nf-core/deseq2/differential/environment.yml +++ b/modules/nf-core/deseq2/differential/environment.yml @@ -1,5 +1,7 @@ +name: deseq2_differential channels: - conda-forge - bioconda + - defaults dependencies: - bioconda::bioconductor-deseq2=1.34.0 diff --git a/modules/nf-core/deseq2/differential/main.nf b/modules/nf-core/deseq2/differential/main.nf index 4d25602f..ab7bc06a 100644 --- a/modules/nf-core/deseq2/differential/main.nf +++ b/modules/nf-core/deseq2/differential/main.nf @@ -30,21 +30,4 @@ process DESEQ2_DIFFERENTIAL { script: template 'deseq_de.R' - - stub: - """ - touch ${meta.id}.deseq2.results.tsv - touch ${meta.id}.deseq2.dispersion.png - touch ${meta.id}.dds.rld.rds - touch ${meta.id}.deseq2.sizefactors.tsv - touch ${meta.id}.normalised_counts.tsv - touch ${meta.id}.rlog.tsv - touch ${meta.id}.deseq2.model.txt - touch ${meta.id}.R_sessionInfo.log - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bioconductor-deseq2: \$(Rscript -e "library(DESeq2); cat(as.character(packageVersion('DESeq2')))") - END_VERSIONS - """ } diff --git a/modules/nf-core/deseq2/differential/meta.yml b/modules/nf-core/deseq2/differential/meta.yml index be8cec47..2b3e33b5 100644 --- a/modules/nf-core/deseq2/differential/meta.yml +++ b/modules/nf-core/deseq2/differential/meta.yml @@ -7,167 +7,102 @@ keywords: - deseq2 tools: - "deseq2": - description: "Differential gene expression analysis based on the negative binomial - distribution" + description: "Differential gene expression analysis based on the negative binomial distribution" homepage: "https://bioconductor.org/packages/release/bioc/html/DESeq2.html" documentation: "https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html" tool_dev_url: "https://github.com/mikelove/DESeq2" doi: "10.1186/s13059-014-0550-8" licence: ["LGPL >=3"] - identifier: biotools:deseq2 input: - - - meta: - type: map - description: | - Groovy Map containing contrast information. This can be used at the - workflow level to pass optional parameters to the module, e.g. - [ id:'contrast1', blocking:'patient' ] passed in as ext.args like: - '--blocking_variable $meta.blocking'. - - contrast_variable: - type: string - description: | - The column in the sample sheet that should be used to define groups for - comparison - - reference: - type: string - description: | - The value within the contrast_variable column of the sample sheet that - should be used to derive the reference samples - - target: - type: string - description: | - The value within the contrast_variable column of the sample sheet that - should be used to derive the target samples - - - meta2: - type: map - description: | - Groovy map containing study-wide metadata related to the sample sheet - and matrix - - samplesheet: - type: file - description: | - CSV or TSV format sample sheet with sample metadata - - counts: - type: file - description: | - Raw TSV or CSV format expression matrix as output from the nf-core - RNA-seq workflow - - - meta3: - type: file - description: | - Meta map describing control genes, e.g. [ id: 'ERCC' ] - - control_genes_file: - type: file - description: | - Text file listing control genes, one per line - - - meta4: - type: map - description: | - Groovy map containing study-wide metadata related to the transcript - lengths file - - transcript_lengths_file: - type: file - description: | - Optional file of transcript lengths, with the same sample columns as - counts. If supplied, lengths will be supplied to DESeq2 to correct for - differences in average transcript lengths across samples. + - meta: + type: map + description: | + Groovy Map containing contrast information. This can be used at the + workflow level to pass optional parameters to the module, e.g. + [ id:'contrast1', blocking:'patient' ] passed in as ext.args like: + '--blocking_variable $meta.blocking'. + - contrast_variable: + type: string + description: | + The column in the sample sheet that should be used to define groups for + comparison + - reference: + type: string + description: | + The value within the contrast_variable column of the sample sheet that + should be used to derive the reference samples + - target: + type: string + description: | + The value within the contrast_variable column of the sample sheet that + should be used to derive the target samples + - meta2: + type: map + description: | + Groovy map containing study-wide metadata related to the sample sheet + and matrix + - samplesheet: + type: file + description: | + CSV or TSV format sample sheet with sample metadata + - counts: + type: file + description: | + Raw TSV or CSV format expression matrix as output from the nf-core + RNA-seq workflow + - meta3: + type: file + description: | + Meta map describing control genes, e.g. [ id: 'ERCC' ] + - control_genes_file: + type: file + description: | + Text file listing control genes, one per line + - meta4: + type: map + description: | + Groovy map containing study-wide metadata related to the transcript + lengths file + - transcript_lengths_file: + type: file + description: | + Optional file of transcript lengths, with the same sample columns as + counts. If supplied, lengths will be supplied to DESeq2 to correct for + differences in average transcript lengths across samples. + output: - results: - - meta: - type: file - description: TSV-format table of differential expression information as output - by DESeq2 - pattern: "deseq2.results.tsv" - - "*.deseq2.results.tsv": - type: file - description: TSV-format table of differential expression information as output - by DESeq2 - pattern: "deseq2.results.tsv" + type: file + description: TSV-format table of differential expression information as output by DESeq2 + pattern: "deseq2.results.tsv" - dispersion_plot: - - meta: - type: file - description: DESeq2 dispersion plot - pattern: "deseq2.dispersion.png" - - "*.deseq2.dispersion.png": - type: file - description: DESeq2 dispersion plot - pattern: "deseq2.dispersion.png" + type: file + description: DESeq2 dispersion plot + pattern: "deseq2.dispersion.png" - rdata: - - meta: - type: file - description: Serialised DESeq2 object - pattern: "dds.rld.rds" - - "*.dds.rld.rds": - type: file - description: Serialised DESeq2 object - pattern: "dds.rld.rds" - - size_factors: - - meta: - type: file - description: Size factors - pattern: "deseq2.sizefactors.tsv" - - "*.deseq2.sizefactors.tsv": - type: file - description: Size factors - pattern: "deseq2.sizefactors.tsv" + type: file + description: Serialised DESeq2 object + pattern: "dds.rld.rds" + - sizefactors: + type: file + description: Size factors + pattern: "deseq2.sizefactors.tsv" - normalised_counts: - - meta: - type: file - description: TSV-format counts matrix, normalised to size factors - pattern: "normalised_counts.tsv" - - "*.normalised_counts.tsv": - type: file - description: TSV-format counts matrix, normalised to size factors - pattern: "normalised_counts.tsv" - - rlog_counts: - - meta: - type: file - description: | - Optional, TSV-format counts matrix, normalised to size factors, with - variance stabilisation applied via `rlog()`. - pattern: "rlog.tsv" - - "*.rlog.tsv": - type: file - description: | - Optional, TSV-format counts matrix, normalised to size factors, with - variance stabilisation applied via `rlog()`. - pattern: "rlog.tsv" - - vst_counts: - - meta: - type: file - description: | - Optional, TSV-format counts matrix, normalised to size factors, with - variance stabilisation applied via `vst()`. - pattern: "vst_counts.tsv" - - "*.vst.tsv": - type: file - description: | - Optional, TSV-format counts matrix, normalised to size factors, with - variance stabilisation applied via `vst()`. - pattern: "vst_counts.tsv" + type: file + description: TSV-format counts matrix, normalised to size factors + pattern: "normalised_counts.tsv" + - variance_stabilised_counts: + type: file + description: TSV-format counts matrix, normalised to size factors, with variance stabilisation applied + pattern: "variance_stabilised_counts.tsv" - model: - - meta: - type: file - description: TXT-format DESeq2 model - pattern: "deseq2.model.tsv" - - "*.deseq2.model.txt": - type: file - description: TXT-format DESeq2 model - pattern: "deseq2.model.tsv" - - session_info: - - meta: - type: file - description: dump of R SessionInfo - pattern: "*.log" - - "*.R_sessionInfo.log": - type: file - description: dump of R SessionInfo - pattern: "*.log" + type: file + description: TXT-format DESeq2 model + pattern: "deseq2.model.tsv" - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/deseq2/differential/templates/deseq_de.R b/modules/nf-core/deseq2/differential/templates/deseq_de.R index 532d7076..a1b3abca 100755 --- a/modules/nf-core/deseq2/differential/templates/deseq_de.R +++ b/modules/nf-core/deseq2/differential/templates/deseq_de.R @@ -68,6 +68,34 @@ read_delim_flexible <- function(file, header = TRUE, row.names = NULL, check.nam ) } +#' Round numeric dataframe columns to fixed decimal places by applying +#' formatting and converting back to numerics +#' +#' @param dataframe A data frame +#' @param columns Which columns to round (assumes all of them by default) +#' @param digits How many decimal places to round to? +#' +#' @return output Data frame + +round_dataframe_columns <- function(df, columns = NULL, digits = 8){ + if (is.null(columns)){ + columns <- colnames(df) + } + + df[,columns] <- format( + data.frame(df[, columns], check.names = FALSE), + nsmall = digits + ) + + # Convert columns back to numeric + + for (c in columns) { + df[[c]][grep("^ *NA\$", df[[c]])] <- NA + df[[c]] <- as.numeric(df[[c]]) + } + df +} + ################################################ ################################################ ## PARSE PARAMETERS FROM NEXTFLOW ## @@ -111,8 +139,7 @@ opt <- list( shrink_lfc = TRUE, cores = 1, vs_blind = TRUE, - vst_nsub = 1000, - round_digits = NULL + vst_nsub = 1000 ) opt_types <- lapply(opt, class) @@ -131,9 +158,6 @@ for ( ao in names(args_opt)){ opt[[ao]] <- args_opt[[ao]] } } -if ( ! is.null(opt\$round_digits)){ - opt\$round_digits <- as.numeric(opt\$round_digits) -} # Check if required parameters have been provided @@ -394,20 +418,14 @@ cat("Saving results for ", contrast.name, " ...\n", sep = "") # Differential expression table- note very limited rounding for consistency of # results -if (! is.null(opt\$round_digits)){ - comp.results <- apply(data.frame(comp.results), 2, function(x) round(x, opt\$round_digits)) -} -comp.results <- `colnames<-`( - data.frame( - gene_id = rownames(comp.results), - comp.results, - check.names = FALSE - ), - c(opt\$gene_id_col, colnames(comp.results)) # Setting all column names +out_df <- cbind( + setNames(data.frame(rownames(comp.results)), opt\$gene_id_col), + round_dataframe_columns( + data.frame(comp.results[, !(colnames(comp.results) %in% opt\$gene_id_col)], check.names = FALSE) + ) ) - write.table( - comp.results, + out_df, file = paste(opt\$output_prefix, 'deseq2.results.tsv', sep = '.'), col.names = TRUE, row.names = FALSE, @@ -448,21 +466,12 @@ write.table( # Write specified matrices -normalised_matrix <- counts(dds, normalized = TRUE) -if (! is.null(opt\$round_digits)){ - normalised_matrix <- apply(normalised_matrix, 2, function(x) round(x, opt\$round_digits)) -} -normalised_matrix <- `colnames<-`( - data.frame( - gene_id = rownames(counts(dds)), # First column with row names from counts(dds) - normalised_matrix, # Other columns - check.names = FALSE - ), - c(opt\$gene_id_col, colnames(normalised_matrix)) # Setting all column names +out_df <- cbind( + setNames(data.frame(rownames(counts(dds))), opt\$gene_id_col), + data.frame(counts(dds, normalized = TRUE)[, !(colnames(counts(dds, normalized = TRUE)) %in% opt\$gene_id_col)], check.names = FALSE) ) - write.table( - normalised_matrix, + out_df, file = paste(opt\$output_prefix, 'normalised_counts.tsv', sep = '.'), col.names = TRUE, row.names = FALSE, @@ -474,26 +483,21 @@ write.table( for (vs_method_name in strsplit(opt\$vs_method, ',')){ if (vs_method_name == 'vst'){ - vs_mat <- assay(vst(dds, blind = opt\$vs_blind, nsub = opt\$vst_nsub)) + vs_mat <- vst(dds, blind = opt\$vs_blind, nsub = opt\$vst_nsub) }else if (vs_method_name == 'rlog'){ - vs_mat <- assay(rlog(dds, blind = opt\$vs_blind, fitType = opt\$fit_type)) + vs_mat <- rlog(dds, blind = opt\$vs_blind, fitType = opt\$fit_type) } - if (! is.null(opt\$round_digits)){ - vs_mat <- apply(vs_mat, 2, function(x) round(x, opt\$round_digits)) - } + # Again apply the slight rounding and then restore numeric - vs_mat <- `colnames<-`( - data.frame( - gene_id = rownames(counts(dds)), # First column with row names from counts(dds) - vs_mat, # Other columns from vs_mat - check.names = FALSE - ), - c(opt\$gene_id_col, colnames(vs_mat)) # Setting all column names + out_df <- cbind( + setNames(data.frame(rownames(counts(dds))), opt\$gene_id_col), + round_dataframe_columns( + data.frame(assay(vs_mat)[, !(colnames(assay(vs_mat)) %in% opt\$gene_id_col)], check.names = FALSE) + ) ) - write.table( - vs_mat, + out_df, file = paste(opt\$output_prefix, vs_method_name, 'tsv', sep = '.'), col.names = TRUE, row.names = FALSE, diff --git a/modules/nf-core/deseq2/differential/tests/contrasts_matrix.config b/modules/nf-core/deseq2/differential/tests/contrasts_matrix.config deleted file mode 100644 index 0e4e63a1..00000000 --- a/modules/nf-core/deseq2/differential/tests/contrasts_matrix.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - withName: 'DESEQ2_DIFFERENTIAL' { - ext.args = { "--round_digits 5 --blocking_variables $meta.blocking --vs_method rlog" } - } -} diff --git a/modules/nf-core/deseq2/differential/tests/contrasts_matrix_exclude_samples.config b/modules/nf-core/deseq2/differential/tests/contrasts_matrix_exclude_samples.config deleted file mode 100644 index bd62f1d7..00000000 --- a/modules/nf-core/deseq2/differential/tests/contrasts_matrix_exclude_samples.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - withName: 'DESEQ2_DIFFERENTIAL' { - ext.args = { "--round_digits 4 --blocking_variables $meta.blocking --vs_method rlog --exclude_samples_col sample_number --exclude_samples_values sample1" } - } -} diff --git a/modules/nf-core/deseq2/differential/tests/contrasts_matrix_noblocking.config b/modules/nf-core/deseq2/differential/tests/contrasts_matrix_noblocking.config deleted file mode 100644 index 77565bca..00000000 --- a/modules/nf-core/deseq2/differential/tests/contrasts_matrix_noblocking.config +++ /dev/null @@ -1,10 +0,0 @@ -process { - withName: 'DESEQ2_DIFFERENTIAL' { - ext.args = { - [ - ((meta.blocking == null) ? '' : "--blocking_variables $meta.blocking"), - "--vs_method rlog --round_digits 5" - ].join(' ').trim() - } - } -} diff --git a/modules/nf-core/deseq2/differential/tests/contrasts_matrix_spikes.config b/modules/nf-core/deseq2/differential/tests/contrasts_matrix_spikes.config deleted file mode 100644 index 5ecf98b0..00000000 --- a/modules/nf-core/deseq2/differential/tests/contrasts_matrix_spikes.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - withName: 'DESEQ2_DIFFERENTIAL' { - ext.args = { "--round_digits 5 --sizefactors_from_controls TRUE --blocking_variables $meta.blocking --vs_method rlog" } - } -} diff --git a/modules/nf-core/deseq2/differential/tests/contrasts_matrix_subset_to_contrast.config b/modules/nf-core/deseq2/differential/tests/contrasts_matrix_subset_to_contrast.config deleted file mode 100644 index 183b37c2..00000000 --- a/modules/nf-core/deseq2/differential/tests/contrasts_matrix_subset_to_contrast.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - withName: 'DESEQ2_DIFFERENTIAL' { - ext.args = { "--round_digits 5 --blocking_variables $meta.blocking --vs_method rlog --subset_to_contrast_samples TRUE" } - } -} diff --git a/modules/nf-core/deseq2/differential/tests/contrasts_matrix_vst_nsub.config b/modules/nf-core/deseq2/differential/tests/contrasts_matrix_vst_nsub.config deleted file mode 100644 index eb7010dd..00000000 --- a/modules/nf-core/deseq2/differential/tests/contrasts_matrix_vst_nsub.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - withName: 'DESEQ2_DIFFERENTIAL' { - ext.args = { "--round_digits 5 --blocking_variables $meta.blocking --vs_method vst --vst_nsub 500" } - } -} diff --git a/modules/nf-core/deseq2/differential/tests/main.nf.test b/modules/nf-core/deseq2/differential/tests/main.nf.test deleted file mode 100644 index 370f05dc..00000000 --- a/modules/nf-core/deseq2/differential/tests/main.nf.test +++ /dev/null @@ -1,499 +0,0 @@ -nextflow_process { - - name "Test Process DESEQ2_DIFFERENTIAL" - script "../main.nf" - process "DESEQ2_DIFFERENTIAL" - - tag "modules" - tag "modules_nfcore" - tag "deseq2" - tag "deseq2/differential" - - test("mouse - contrasts - matrix") { - - config './contrasts_matrix.config' - - when { - process { - """ - expression_test_data_dir = params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/' - - ch_contrasts = Channel.fromPath(file(expression_test_data_dir + 'SRP254919.contrasts.csv', checkIfExists: true)) - .splitCsv ( header:true, sep:',' ) - .map{ - tuple(it, it.variable, it.reference, it.target) - } - ch_matrix = [ - [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 - input[3] = ch_lengths - """ - } - } - then { - assertAll( - { assert process.success }, - { assert snapshot( - process.out.results, - process.out.size_factors, - process.out.normalised_counts, - process.out.rlog_counts, - process.out.vst_counts, - process.out.model, - process.out.versions, - 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") } - ) - } - } - - test("mouse - contrasts - matrix - lengths") { - - config './contrasts_matrix.config' - - when { - process { - """ - expression_test_data_dir = params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/' - - ch_contrasts = Channel.fromPath(file(expression_test_data_dir + 'SRP254919.contrasts.csv', checkIfExists: true)) - .splitCsv ( header:true, sep:',' ) - .map{ - tuple(it, it.variable, it.reference, it.target) - } - ch_matrix = [ - [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'], - file(expression_test_data_dir + 'SRP254919.spoofed_lengths.tsv', checkIfExists: true) - ] - - ch_spikes = [[],[]] - - input[0] = ch_contrasts - input[1] = ch_matrix - input[2] = ch_spikes - input[3] = ch_lengths - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot( - process.out.results, - process.out.size_factors, - process.out.normalised_counts, - process.out.rlog_counts, - process.out.vst_counts, - process.out.model, - process.out.versions, - 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") } - ) - } - - } - - test("mouse - contrasts - matrix - no blocking") { - - config './contrasts_matrix_noblocking.config' - - when { - process { - """ - expression_test_data_dir = params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/' - - ch_contrasts = Channel.fromPath(file(expression_test_data_dir + 'SRP254919.contrasts.csv', checkIfExists: true)) - .splitCsv ( header:true, sep:',' ) - .map{ - tuple(it, it.variable, it.reference, it.target) - } - ch_matrix = [ - [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 - input[3] = ch_lengths - """ - } - } - then { - assertAll( - { assert process.success }, - { assert snapshot( - process.out.results, - process.out.size_factors, - process.out.normalised_counts, - process.out.rlog_counts, - process.out.vst_counts, - process.out.model, - process.out.versions, - 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") } - ) - } - } - - test("mouse - contrasts - matrix - spikes") { - - config './contrasts_matrix_spikes.config' - - when { - process { - """ - expression_test_data_dir = params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/' - - ch_contrasts = Channel.fromPath(file(expression_test_data_dir + 'SRP254919.contrasts.csv', checkIfExists: true)) - .splitCsv ( header:true, sep:',' ) - .map{ - tuple(it, it.variable, it.reference, it.target) - } - ch_matrix = [ - [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'], - file(expression_test_data_dir + 'SRP254919.spikes.tsv', checkIfExists: true) - ] - ch_lengths = [[],[]] - - input[0] = ch_contrasts - input[1] = ch_matrix - input[2] = ch_spikes - input[3] = ch_lengths - """ - } - } - then { - assertAll( - { assert process.success }, - { assert snapshot( - process.out.results, - process.out.size_factors, - process.out.normalised_counts, - process.out.rlog_counts, - process.out.vst_counts, - process.out.model, - process.out.versions, - 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") } - ) - } - } - - test("mouse - contrasts - matrix - strip spikes") { - - config './contrasts_matrix.config' - - when { - process { - """ - expression_test_data_dir = params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/' - - ch_contrasts = Channel.fromPath(file(expression_test_data_dir + 'SRP254919.contrasts.csv', checkIfExists: true)) - .splitCsv ( header:true, sep:',' ) - .map{ - tuple(it, it.variable, it.reference, it.target) - } - ch_matrix = [ - [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'], - file(expression_test_data_dir + 'SRP254919.spikes.tsv', checkIfExists: true) - ] - ch_lengths = [[],[]] - - input[0] = ch_contrasts - input[1] = ch_matrix - input[2] = ch_spikes - input[3] = ch_lengths - """ - } - } - then { - assertAll( - { assert process.success }, - { assert snapshot( - process.out.results, - process.out.size_factors, - process.out.normalised_counts, - process.out.rlog_counts, - process.out.vst_counts, - process.out.model, - process.out.versions, - 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") } - ) - } - } - - test("mouse - contrasts - matrix - csv") { - - config './contrasts_matrix.config' - - when { - process { - """ - expression_test_data_dir = params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/' - - ch_contrasts = Channel.fromPath(file(expression_test_data_dir + 'SRP254919.contrasts.csv', checkIfExists: true)) - .splitCsv ( header:true, sep:',' ) - .map{ - tuple(it, it.variable, it.reference, it.target) - } - - // Convert the matrix to a CSV first - ch_matrix = Channel.fromPath(expression_test_data_dir + 'SRP254919.salmon.merged.gene_counts.top1000cov.tsv') - .splitCsv(header: false) - .map{ - it.join('\t') - } - .collectFile(name: 'test.tsv', newLine: true, sort: false) - .map{ - [ [ id:'test'], file(expression_test_data_dir + 'SRP254919.samplesheet.csv', checkIfExists: true), it] - } - ch_spikes = [[],[]] - ch_lengths = [[],[]] - - input[0] = ch_contrasts - input[1] = ch_matrix - input[2] = ch_spikes - input[3] = ch_lengths - """ - } - } - then { - assertAll( - { assert process.success }, - { assert snapshot( - process.out.results, - process.out.size_factors, - process.out.normalised_counts, - process.out.rlog_counts, - process.out.vst_counts, - process.out.model, - process.out.versions, - 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") } - ) - } - } - - test("mouse - contrasts - matrix - vst nsub") { - - config './contrasts_matrix_vst_nsub.config' - - when { - process { - """ - expression_test_data_dir = params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/' - - ch_contrasts = Channel.fromPath(file(expression_test_data_dir + 'SRP254919.contrasts.csv', checkIfExists: true)) - .splitCsv ( header:true, sep:',' ) - .map{ - tuple(it, it.variable, it.reference, it.target) - } - ch_matrix = [ - [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 - input[3] = ch_lengths - """ - } - } - then { - assertAll( - { assert process.success }, - { assert snapshot( - process.out.results, - process.out.size_factors, - process.out.normalised_counts, - process.out.rlog_counts, - process.out.vst_counts, - process.out.model, - process.out.versions, - 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") } - ) - } - } - - test("mouse - contrasts - matrix - subset to contrast") { - - config './contrasts_matrix_subset_to_contrast.config' - - when { - process { - """ - expression_test_data_dir = params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/' - - ch_contrasts = Channel.fromPath(file(expression_test_data_dir + 'SRP254919.contrasts.csv', checkIfExists: true)) - .splitCsv ( header:true, sep:',' ) - .map{ - tuple(it, it.variable, it.reference, it.target) - } - ch_matrix = [ - [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 - input[3] = ch_lengths - """ - } - } - then { - assertAll( - { assert process.success }, - { assert snapshot( - process.out.results, - process.out.size_factors, - process.out.normalised_counts, - process.out.rlog_counts, - process.out.vst_counts, - process.out.model, - process.out.versions, - 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") } - ) - } - } - - test("mouse - contrasts - matrix - exclude samples") { - - config './contrasts_matrix_exclude_samples.config' - - when { - process { - """ - expression_test_data_dir = params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/' - - ch_contrasts = Channel.fromPath(file(expression_test_data_dir + 'SRP254919.contrasts.csv', checkIfExists: true)) - .splitCsv ( header:true, sep:',' ) - .map{ - tuple(it, it.variable, it.reference, it.target) - } - ch_matrix = [ - [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 - input[3] = ch_lengths - """ - } - } - then { - assertAll( - { assert process.success }, - { assert snapshot( - process.out.results, - process.out.size_factors, - process.out.normalised_counts, - process.out.rlog_counts, - process.out.vst_counts, - process.out.model, - process.out.versions, - 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") } - ) - } - } - test("mouse - contrasts - matrix - stub") { - - config './contrasts_matrix.config' - - options "-stub" - - when { - process { - """ - expression_test_data_dir = params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/' - - ch_contrasts = Channel.fromPath(file(expression_test_data_dir + 'SRP254919.contrasts.csv', checkIfExists: true)) - .splitCsv ( header:true, sep:',' ) - .map{ - tuple(it, it.variable, it.reference, it.target) - } - ch_matrix = [ - [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 - input[3] = ch_lengths - """ - } - } - then { - assertAll( - { assert process.success }, - { assert snapshot( process.out).match() } - ) - } - } -} diff --git a/modules/nf-core/deseq2/differential/tests/main.nf.test.snap b/modules/nf-core/deseq2/differential/tests/main.nf.test.snap deleted file mode 100644 index 84f14f20..00000000 --- a/modules/nf-core/deseq2/differential/tests/main.nf.test.snap +++ /dev/null @@ -1,1480 +0,0 @@ -{ - 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], - [ - { - "id": "treatment_mCherry_hND6_sample_number", - "variable": "treatment", - "reference": "mCherry", - "target": "hND6", - "blocking": "sample_number" - }, - "treatment_mCherry_hND6_sample_number.rlog.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "session_info": [ - [ - { - "id": "treatment_mCherry_hND6_", - "variable": "treatment", - "reference": "mCherry", - "target": "hND6", - "blocking": "" - }, - "treatment_mCherry_hND6_.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - [ - { - "id": "treatment_mCherry_hND6_sample_number", - "variable": "treatment", - "reference": "mCherry", - "target": "hND6", - "blocking": "sample_number" - }, - "treatment_mCherry_hND6_sample_number.R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "size_factors": [ - [ - { - "id": "treatment_mCherry_hND6_", - "variable": "treatment", - "reference": "mCherry", - "target": "hND6", - "blocking": "" - }, - "treatment_mCherry_hND6_.deseq2.sizefactors.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - [ - { - "id": "treatment_mCherry_hND6_sample_number", - "variable": "treatment", - "reference": "mCherry", - "target": "hND6", - "blocking": "sample_number" - }, - "treatment_mCherry_hND6_sample_number.deseq2.sizefactors.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,2d67217d8adb1fa0d143b4017e6657fe", - "versions.yml:md5,2d67217d8adb1fa0d143b4017e6657fe" - ], - "vst_counts": [ - - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-04-18T15:55:53.660457322" - } -} \ No newline at end of file diff --git a/modules/nf-core/deseq2/differential/tests/tags.yml b/modules/nf-core/deseq2/differential/tests/tags.yml deleted file mode 100644 index 8407e5c6..00000000 --- a/modules/nf-core/deseq2/differential/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -deseq2/differential: - - "modules/nf-core/deseq2/differential/**" diff --git a/tests/test.nf.test.snap b/tests/test.nf.test.snap index 4b14b57c..022c9d5a 100644 --- a/tests/test.nf.test.snap +++ b/tests/test.nf.test.snap @@ -174,18 +174,18 @@ "app.R:md5,bedcfc45b6cdcc2b8fe3627987e2b17a", "versions.yml:md5,892774f9d56ba10c8646736b7f777ecc", "Mus_musculus.anno.tsv:md5,c1d7f21e64bd00f845ec6545c123a1fb", - "treatment_mCherry_hND6_.deseq2.results.tsv:md5,b40bd97367cce0fc3926a722136bd936", - "treatment_mCherry_hND6_.deseq2.results_filtered.tsv:md5,b5560b6ccd18f09cb514d0b328448e0a", - "treatment_mCherry_hND6_sample_number.deseq2.results.tsv:md5,00303655a04cc0b3671932d6cb5011dc", - "treatment_mCherry_hND6_sample_number.deseq2.results_filtered.tsv:md5,08f3bb3a6c6abcd27c096f12c15c974c", + "treatment_mCherry_hND6_.deseq2.results.tsv:md5,42ad391a5d3b2e4e7931af3088cc6400", + "treatment_mCherry_hND6_.deseq2.results_filtered.tsv:md5,cd67e101a9f0edf196ee0cd8491f8774", + "treatment_mCherry_hND6_sample_number.deseq2.results.tsv:md5,b41cbaacd04a25b45295f3f987ff7500", + "treatment_mCherry_hND6_sample_number.deseq2.results_filtered.tsv:md5,98fa3ec0992859d2a524ecce1259f0ed", "all.normalised_counts.tsv:md5,1d7ad0c02b483f2eff1a5b357a74d011", - "all.vst.tsv:md5,2fa9f1008e3536b049ca69d48bbe8fbd" + "all.vst.tsv:md5,a08d06d3c3218619b7bd85beead467bd" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.10.2" }, - "timestamp": "2024-12-03T17:05:32.173242283" + "timestamp": "2024-12-04T14:36:19.54228835" } } \ No newline at end of file diff --git a/tests/test_affy.nf.test.snap b/tests/test_affy.nf.test.snap index c98040ff..b8976dd7 100644 --- a/tests/test_affy.nf.test.snap +++ b/tests/test_affy.nf.test.snap @@ -236,6 +236,6 @@ "nf-test": "0.9.0", "nextflow": "24.10.2" }, - "timestamp": "2024-12-03T19:58:11.092290214" + "timestamp": "2024-12-04T14:40:06.384330301" } } \ No newline at end of file diff --git a/tests/test_maxquant.nf.test.snap b/tests/test_maxquant.nf.test.snap index 3782d8e2..fd6fc549 100644 --- a/tests/test_maxquant.nf.test.snap +++ b/tests/test_maxquant.nf.test.snap @@ -171,8 +171,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.10.0" + "nextflow": "24.10.2" }, - "timestamp": "2024-11-17T21:32:05.655955914" + "timestamp": "2024-12-04T14:41:27.89777414" } } \ No newline at end of file diff --git a/tests/test_nogtf.nf.test.snap b/tests/test_nogtf.nf.test.snap index 14ebf2ba..c4b289d4 100644 --- a/tests/test_nogtf.nf.test.snap +++ b/tests/test_nogtf.nf.test.snap @@ -90,18 +90,18 @@ "treatment_mCherry_hND6_sample_number.deseq2.dispersion.png:md5,d0f07f97c7f5c660b173d85b85ed50b9", "app.R:md5,bedcfc45b6cdcc2b8fe3627987e2b17a", "versions.yml:md5,892774f9d56ba10c8646736b7f777ecc", - "treatment_mCherry_hND6_.deseq2.results.tsv:md5,4726dd3c33edce84d6356079c578bbd4", - "treatment_mCherry_hND6_.deseq2.results_filtered.tsv:md5,5c23f53046190eabce927cc968abed34", - "treatment_mCherry_hND6_sample_number.deseq2.results.tsv:md5,119c986fd9235ae6a6c88ed1dd4d0a3d", - "treatment_mCherry_hND6_sample_number.deseq2.results_filtered.tsv:md5,6d969a3049ba16f8f12fc8abeb2b9899", + "treatment_mCherry_hND6_.deseq2.results.tsv:md5,d9e894aeb89aa5bc79bf7ce31304d7c0", + "treatment_mCherry_hND6_.deseq2.results_filtered.tsv:md5,630820ec91287d8bcb2e5882431c09c3", + "treatment_mCherry_hND6_sample_number.deseq2.results.tsv:md5,02b1c8f3c2987b0cb1a64913dd90bf26", + "treatment_mCherry_hND6_sample_number.deseq2.results_filtered.tsv:md5,1e1c8edb0aa5acee308bc1fc81d1aa16", "all.normalised_counts.tsv:md5,e960aa685547a3ea778523da84fae136", - "all.vst.tsv:md5,8e19361180daa5a68de6f099b9093a8c" + "all.vst.tsv:md5,ea4e437ee57b2c5ef8c19d427656e3c6" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.10.2" }, - "timestamp": "2024-12-03T17:13:45.527625008" + "timestamp": "2024-12-04T14:42:50.203829645" } } \ No newline at end of file diff --git a/tests/test_rnaseq_limma.nf.test.snap b/tests/test_rnaseq_limma.nf.test.snap index d3195034..682cdfa7 100644 --- a/tests/test_rnaseq_limma.nf.test.snap +++ b/tests/test_rnaseq_limma.nf.test.snap @@ -175,8 +175,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.10.0" + "nextflow": "24.10.2" }, - "timestamp": "2024-11-17T21:37:45.162699026" + "timestamp": "2024-12-04T14:45:14.298568994" } } \ No newline at end of file diff --git a/tests/test_soft.nf.test.snap b/tests/test_soft.nf.test.snap index a0f14b37..2415a050 100644 --- a/tests/test_soft.nf.test.snap +++ b/tests/test_soft.nf.test.snap @@ -94,6 +94,6 @@ "nf-test": "0.9.0", "nextflow": "24.10.2" }, - "timestamp": "2024-12-03T17:18:11.428945243" + "timestamp": "2024-12-04T14:46:53.576053465" } } \ No newline at end of file