From 291f9bf3866434841bb56f5c4003812ab30c2539 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 25 Jul 2023 08:47:45 +0100 Subject: [PATCH] R differential modules control over output prefixes (#3664) * R differential modules control over output prefixes * Set differential module prefixes * Actually we need to do prefix handling within the template * Set differential module prefixes * Fix test files for new prefix specification * Add meta to limma test * Fix DESeq2 tests * fix remaining tests for limma * Update grep to fix broken solve * Try bumping affy * Use new build * update md5sum for annotation --- modules/nf-core/affy/justrma/main.nf | 6 +- .../deseq2/differential/templates/deseq_de.R | 21 ++- .../limma/differential/templates/limma_de.R | 15 +-- modules/nf-core/untar/main.nf | 2 +- tests/modules/nf-core/affy/justrma/test.yml | 2 +- .../nf-core/deseq2/differential/test.yml | 120 +++++++++--------- .../nf-core/limma/differential/main.nf | 6 +- .../nf-core/limma/differential/test.yml | 24 ++-- 8 files changed, 95 insertions(+), 101 deletions(-) diff --git a/modules/nf-core/affy/justrma/main.nf b/modules/nf-core/affy/justrma/main.nf index 40ebcbf1847..d0da712948f 100644 --- a/modules/nf-core/affy/justrma/main.nf +++ b/modules/nf-core/affy/justrma/main.nf @@ -2,10 +2,10 @@ process AFFY_JUSTRMA { tag "$meta.id" label 'process_single' - conda "bioconda::bioconductor-affy=1.76.0" + conda "bioconda::bioconductor-affy=1.78.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bioconductor-affy:1.76.0--r42hc0cfd56_2': - 'biocontainers/bioconductor-affy:1.76.0--r42hc0cfd56_2' }" + 'https://depot.galaxyproject.org/singularity/bioconductor-affy:1.78.0--r43ha9d7317_1': + 'biocontainers/bioconductor-affy:1.78.0--r43ha9d7317_1' }" input: tuple val(meta), path(samplesheet), path(celfiles_dir) diff --git a/modules/nf-core/deseq2/differential/templates/deseq_de.R b/modules/nf-core/deseq2/differential/templates/deseq_de.R index f1fcd847349..0c7ea82d5bc 100755 --- a/modules/nf-core/deseq2/differential/templates/deseq_de.R +++ b/modules/nf-core/deseq2/differential/templates/deseq_de.R @@ -93,6 +93,7 @@ round_dataframe_columns <- function(df, columns = NULL, digits = 8){ # Set defaults and classes opt <- list( + output_prefix = ifelse('$task.ext.prefix' == 'null', '$meta.id', '$task.ext.prefix'), count_file = '$counts', sample_file = '$samplesheet', contrast_variable = '$contrast_variable', @@ -143,7 +144,7 @@ for ( ao in names(args_opt)){ # Check if required parameters have been provided -required_opts <- c('contrast_variable', 'reference_level', 'target_level') +required_opts <- c('contrast_variable', 'reference_level', 'target_level', 'output_prefix') missing <- required_opts[unlist(lapply(opt[required_opts], is.null)) | ! required_opts %in% names(opt)] if (length(missing) > 0){ @@ -369,10 +370,6 @@ if (opt\$shrink_lfc){ ################################################ ################################################ -prefix_part_names <- c('contrast_variable', 'reference_level', 'target_level', 'blocking_variables') -prefix_parts <- unlist(lapply(prefix_part_names, function(x) gsub("[^[:alnum:]]", "_", opt[[x]]))) -output_prefix <- paste(prefix_parts[prefix_parts != ''], collapse = '-') - contrast.name <- paste(opt\$target_level, opt\$reference_level, sep = "_vs_") cat("Saving results for ", contrast.name, " ...\n", sep = "") @@ -386,7 +383,7 @@ write.table( round_dataframe_columns(data.frame(comp.results, check.names = FALSE)), check.names = FALSE ), - file = paste(output_prefix, 'deseq2.results.tsv', sep = '.'), + file = paste(opt\$output_prefix, 'deseq2.results.tsv', sep = '.'), col.names = TRUE, row.names = FALSE, sep = '\t', @@ -396,7 +393,7 @@ write.table( # Dispersion plot png( - file = paste(output_prefix, 'deseq2.dispersion.png', sep = '.'), + file = paste(opt\$output_prefix, 'deseq2.dispersion.png', sep = '.'), width = 600, height = 600 ) @@ -405,7 +402,7 @@ dev.off() # R object for other processes to use -saveRDS(dds, file = paste(output_prefix, 'dds.rld.rds', sep = '.')) +saveRDS(dds, file = paste(opt\$output_prefix, 'dds.rld.rds', sep = '.')) # Size factors @@ -417,7 +414,7 @@ sf_df = data.frame( colnames(sf_df) <- c('sample', 'sizeFactor') write.table( sf_df, - file = paste(output_prefix, 'deseq2.sizefactors.tsv', sep = '.'), + file = paste(opt\$output_prefix, 'deseq2.sizefactors.tsv', sep = '.'), col.names = TRUE, row.names = FALSE, sep = '\t', @@ -432,7 +429,7 @@ write.table( counts(dds, normalized = TRUE), check.names = FALSE ), - file = paste(output_prefix, 'normalised_counts.tsv', sep = '.'), + file = paste(opt\$output_prefix, 'normalised_counts.tsv', sep = '.'), col.names = TRUE, row.names = FALSE, sep = '\t', @@ -458,7 +455,7 @@ for (vs_method_name in strsplit(opt\$vs_method, ',')){ ), check.names = FALSE ), - file = paste(output_prefix, vs_method_name,'tsv', sep = '.'), + file = paste(opt\$output_prefix, vs_method_name,'tsv', sep = '.'), col.names = TRUE, row.names = FALSE, sep = '\t', @@ -472,7 +469,7 @@ for (vs_method_name in strsplit(opt\$vs_method, ',')){ ################################################ ################################################ -sink(paste(output_prefix, "R_sessionInfo.log", sep = '.')) +sink(paste(opt\$output_prefix, "R_sessionInfo.log", sep = '.')) print(sessionInfo()) sink() diff --git a/modules/nf-core/limma/differential/templates/limma_de.R b/modules/nf-core/limma/differential/templates/limma_de.R index 47d0424f6c7..5a80eb22923 100755 --- a/modules/nf-core/limma/differential/templates/limma_de.R +++ b/modules/nf-core/limma/differential/templates/limma_de.R @@ -65,6 +65,7 @@ read_delim_flexible <- function(file, header = TRUE, row.names = NULL, check.nam # Set defaults and classes opt <- list( + output_prefix = ifelse('$task.ext.prefix' == 'null', '$meta.id', '$task.ext.prefix'), count_file = '$intensities', sample_file = '$samplesheet', contrast_variable = '$contrast_variable', @@ -111,7 +112,7 @@ for ( ao in names(args_opt)){ # Check if required parameters have been provided -required_opts <- c('contrast_variable', 'reference_level', 'target_level') +required_opts <- c('contrast_variable', 'reference_level', 'target_level', 'output_prefix') missing <- required_opts[unlist(lapply(opt[required_opts], is.null)) | ! required_opts %in% names(opt)] if (length(missing) > 0){ @@ -340,10 +341,6 @@ comp.results <- do.call(topTable, toptable_args)[rownames(intensities.table),] ################################################ ################################################ -prefix_part_names <- c('contrast_variable', 'reference_level', 'target_level', 'blocking_variables') -prefix_parts <- unlist(lapply(prefix_part_names, function(x) gsub("[^[:alnum:]]", "_", opt[[x]]))) -output_prefix <- paste(prefix_parts[prefix_parts != ''], collapse = '-') - contrast.name <- paste(opt\$target_level, opt\$reference_level, sep = "_vs_") cat("Saving results for ", contrast.name, " ...\n", sep = "") @@ -356,7 +353,7 @@ write.table( probe_id = rownames(comp.results), comp.results ), - file = paste(output_prefix, 'limma.results.tsv', sep = '.'), + file = paste(opt\$output_prefix, 'limma.results.tsv', sep = '.'), col.names = TRUE, row.names = FALSE, sep = '\t', @@ -366,7 +363,7 @@ write.table( # Dispersion plot png( - file = paste(output_prefix, 'limma.mean_difference.png', sep = '.'), + file = paste(opt\$output_prefix, 'limma.mean_difference.png', sep = '.'), width = 600, height = 600 ) @@ -375,7 +372,7 @@ dev.off() # R object for other processes to use -saveRDS(fit2, file = paste(output_prefix, 'MArrayLM.limma.rds', sep = '.')) +saveRDS(fit2, file = paste(opt\$output_prefix, 'MArrayLM.limma.rds', sep = '.')) ################################################ ################################################ @@ -383,7 +380,7 @@ saveRDS(fit2, file = paste(output_prefix, 'MArrayLM.limma.rds', sep = '.')) ################################################ ################################################ -sink(paste(output_prefix, "R_sessionInfo.log", sep = '.')) +sink(paste(opt\$output_prefix, "R_sessionInfo.log", sep = '.')) print(sessionInfo()) sink() diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index 8cd1856c71d..61461c39177 100644 --- a/modules/nf-core/untar/main.nf +++ b/modules/nf-core/untar/main.nf @@ -2,7 +2,7 @@ process UNTAR { tag "$archive" label 'process_single' - conda "conda-forge::sed=4.7 bioconda::grep=3.4 conda-forge::tar=1.34" + conda "conda-forge::sed=4.7 conda-forge::grep=3.11 conda-forge::tar=1.34" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : 'nf-core/ubuntu:20.04' }" diff --git a/tests/modules/nf-core/affy/justrma/test.yml b/tests/modules/nf-core/affy/justrma/test.yml index 516a0ea6c7c..01b9b7374c7 100644 --- a/tests/modules/nf-core/affy/justrma/test.yml +++ b/tests/modules/nf-core/affy/justrma/test.yml @@ -6,7 +6,7 @@ files: - path: output/affy/normalised.eset.rds - path: output/affy/hgu133a2.annotation.tsv - md5sum: b718d6ff9f3037cf398d7ef7ea03a84d + md5sum: ffe59c061c8e304966f5f8156fb41805 - path: output/affy/normalised.matrix.tsv md5sum: 462665542e9531f6d8993b745ce78ae4 - path: output/affy/versions.yml diff --git a/tests/modules/nf-core/deseq2/differential/test.yml b/tests/modules/nf-core/deseq2/differential/test.yml index 3fd1f45150e..e878d56e20c 100644 --- a/tests/modules/nf-core/deseq2/differential/test.yml +++ b/tests/modules/nf-core/deseq2/differential/test.yml @@ -4,21 +4,21 @@ - deseq2 - deseq2/differential files: - - path: output/deseq2/treatment-mCherry-hND6-sample_number.deseq2.results.tsv + - path: output/deseq2/treatment_mCherry_hND6_sample_number.deseq2.results.tsv md5sum: 86f0312a4691dfb4d7c15643059d8fb8 - - path: output/deseq2/treatment-mCherry-hND6-sample_number.deseq2.sizefactors.tsv + - path: output/deseq2/treatment_mCherry_hND6_sample_number.deseq2.sizefactors.tsv md5sum: 6332f21889ecac387bb12eeb04f23849 - - path: output/deseq2/treatment-mCherry-hND6-sample_number.normalised_counts.tsv + - path: output/deseq2/treatment_mCherry_hND6_sample_number.normalised_counts.tsv md5sum: 827cdf01f366d72d6e4b500e9862ba74 - - path: output/deseq2/treatment-mCherry-hND6-sample_number.rlog.tsv + - path: output/deseq2/treatment_mCherry_hND6_sample_number.rlog.tsv md5sum: 1077cf03a8c6a155932eaaed7415b74c - - path: output/deseq2/treatment-mCherry-hND6.deseq2.results.tsv + - path: output/deseq2/treatment_mCherry_hND6_.deseq2.results.tsv md5sum: 4034522732d975951c79731acc1c9731 - - path: output/deseq2/treatment-mCherry-hND6.deseq2.sizefactors.tsv + - path: output/deseq2/treatment_mCherry_hND6_.deseq2.sizefactors.tsv md5sum: 6332f21889ecac387bb12eeb04f23849 - - path: output/deseq2/treatment-mCherry-hND6.normalised_counts.tsv + - path: output/deseq2/treatment_mCherry_hND6_.normalised_counts.tsv md5sum: 827cdf01f366d72d6e4b500e9862ba74 - - path: output/deseq2/treatment-mCherry-hND6.rlog.tsv + - path: output/deseq2/treatment_mCherry_hND6_.rlog.tsv md5sum: 1077cf03a8c6a155932eaaed7415b74c - name: deseq2 differential test_deseq2_differential_noblocking @@ -27,13 +27,13 @@ - deseq2 - deseq2/differential files: - - path: output/deseq2/treatment-mCherry-hND6.deseq2.results.tsv + - path: output/deseq2/treatment_mCherry_hND6_.deseq2.results.tsv md5sum: 4034522732d975951c79731acc1c9731 - - path: output/deseq2/treatment-mCherry-hND6.deseq2.sizefactors.tsv + - path: output/deseq2/treatment_mCherry_hND6_.deseq2.sizefactors.tsv md5sum: 6332f21889ecac387bb12eeb04f23849 - - path: output/deseq2/treatment-mCherry-hND6.normalised_counts.tsv + - path: output/deseq2/treatment_mCherry_hND6_.normalised_counts.tsv md5sum: 827cdf01f366d72d6e4b500e9862ba74 - - path: output/deseq2/treatment-mCherry-hND6.rlog.tsv + - path: output/deseq2/treatment_mCherry_hND6_.rlog.tsv md5sum: 1077cf03a8c6a155932eaaed7415b74c - name: deseq2 differential test_deseq2_differential_spikes @@ -42,21 +42,21 @@ - deseq2 - deseq2/differential files: - - path: output/deseq2/treatment-mCherry-hND6-sample_number.deseq2.results.tsv + - path: output/deseq2/treatment_mCherry_hND6_sample_number.deseq2.results.tsv md5sum: 150a32eef482244b47ddc7f7ffb1ad2a - - path: output/deseq2/treatment-mCherry-hND6-sample_number.deseq2.sizefactors.tsv + - path: output/deseq2/treatment_mCherry_hND6_sample_number.deseq2.sizefactors.tsv md5sum: 1708374146b4e8c28fbc78fa292102cd - - path: output/deseq2/treatment-mCherry-hND6-sample_number.normalised_counts.tsv + - path: output/deseq2/treatment_mCherry_hND6_sample_number.normalised_counts.tsv md5sum: 1c9c7ee4ca90ff0d91ae16dbfd64fdc9 - - path: output/deseq2/treatment-mCherry-hND6-sample_number.rlog.tsv + - path: output/deseq2/treatment_mCherry_hND6_sample_number.rlog.tsv md5sum: c28300837df9ca6adeba2a52ea5e181e - - path: output/deseq2/treatment-mCherry-hND6.deseq2.results.tsv + - path: output/deseq2/treatment_mCherry_hND6_.deseq2.results.tsv md5sum: 88b3230c5a4ad8717c1d0b38c824f1fc - - path: output/deseq2/treatment-mCherry-hND6.deseq2.sizefactors.tsv + - path: output/deseq2/treatment_mCherry_hND6_.deseq2.sizefactors.tsv md5sum: 1708374146b4e8c28fbc78fa292102cd - - path: output/deseq2/treatment-mCherry-hND6.normalised_counts.tsv + - path: output/deseq2/treatment_mCherry_hND6_.normalised_counts.tsv md5sum: 1c9c7ee4ca90ff0d91ae16dbfd64fdc9 - - path: output/deseq2/treatment-mCherry-hND6.rlog.tsv + - path: output/deseq2/treatment_mCherry_hND6_.rlog.tsv md5sum: c28300837df9ca6adeba2a52ea5e181e - path: output/spoof/spikes.txt md5sum: 8bd8a80b4616fc0a68f69bee6869c8bc @@ -67,21 +67,21 @@ - deseq2 - deseq2/differential files: - - path: output/deseq2/treatment-mCherry-hND6-sample_number.deseq2.results.tsv + - path: output/deseq2/treatment_mCherry_hND6_sample_number.deseq2.results.tsv md5sum: 23de450bda331e7b9330dfd66042a309 - - path: output/deseq2/treatment-mCherry-hND6-sample_number.deseq2.sizefactors.tsv + - path: output/deseq2/treatment_mCherry_hND6_sample_number.deseq2.sizefactors.tsv md5sum: a526a1bb5cb270f5a4a1641fefd289b3 - - path: output/deseq2/treatment-mCherry-hND6-sample_number.normalised_counts.tsv + - path: output/deseq2/treatment_mCherry_hND6_sample_number.normalised_counts.tsv md5sum: bb916c41f91b2ddcc9607619a023ef44 - - path: output/deseq2/treatment-mCherry-hND6-sample_number.rlog.tsv + - path: output/deseq2/treatment_mCherry_hND6_sample_number.rlog.tsv contains: ["ENSMUSG00000036480\t4.01671566\t4.29840714\t5.04221558\t3.09476385\t3.56634694\t5.04719582"] - - path: output/deseq2/treatment-mCherry-hND6.deseq2.results.tsv + - path: output/deseq2/treatment_mCherry_hND6_.deseq2.results.tsv md5sum: 7a385151de48430e592dbcc72c0d0d75 - - path: output/deseq2/treatment-mCherry-hND6.deseq2.sizefactors.tsv + - path: output/deseq2/treatment_mCherry_hND6_.deseq2.sizefactors.tsv md5sum: a526a1bb5cb270f5a4a1641fefd289b3 - - path: output/deseq2/treatment-mCherry-hND6.normalised_counts.tsv + - path: output/deseq2/treatment_mCherry_hND6_.normalised_counts.tsv md5sum: bb916c41f91b2ddcc9607619a023ef44 - - path: output/deseq2/treatment-mCherry-hND6.rlog.tsv + - path: output/deseq2/treatment_mCherry_hND6_.rlog.tsv contains: ["ENSMUSG00000036480\t4.01671566\t4.29840714\t5.04221558\t3.09476385\t3.56634694\t5.04719582"] - path: output/spoof/spikes.txt md5sum: 8bd8a80b4616fc0a68f69bee6869c8bc @@ -92,21 +92,21 @@ - deseq2 - deseq2/differential files: - - path: output/deseq2/treatment-mCherry-hND6-sample_number.deseq2.results.tsv + - path: output/deseq2/treatment_mCherry_hND6_sample_number.deseq2.results.tsv md5sum: 86f0312a4691dfb4d7c15643059d8fb8 - - path: output/deseq2/treatment-mCherry-hND6-sample_number.deseq2.sizefactors.tsv + - path: output/deseq2/treatment_mCherry_hND6_sample_number.deseq2.sizefactors.tsv md5sum: 6332f21889ecac387bb12eeb04f23849 - - path: output/deseq2/treatment-mCherry-hND6-sample_number.normalised_counts.tsv + - path: output/deseq2/treatment_mCherry_hND6_sample_number.normalised_counts.tsv md5sum: 827cdf01f366d72d6e4b500e9862ba74 - - path: output/deseq2/treatment-mCherry-hND6-sample_number.rlog.tsv + - path: output/deseq2/treatment_mCherry_hND6_sample_number.rlog.tsv md5sum: 1077cf03a8c6a155932eaaed7415b74c - - path: output/deseq2/treatment-mCherry-hND6.deseq2.results.tsv + - path: output/deseq2/treatment_mCherry_hND6_.deseq2.results.tsv md5sum: 4034522732d975951c79731acc1c9731 - - path: output/deseq2/treatment-mCherry-hND6.deseq2.sizefactors.tsv + - path: output/deseq2/treatment_mCherry_hND6_.deseq2.sizefactors.tsv md5sum: 6332f21889ecac387bb12eeb04f23849 - - path: output/deseq2/treatment-mCherry-hND6.normalised_counts.tsv + - path: output/deseq2/treatment_mCherry_hND6_.normalised_counts.tsv md5sum: 827cdf01f366d72d6e4b500e9862ba74 - - path: output/deseq2/treatment-mCherry-hND6.rlog.tsv + - path: output/deseq2/treatment_mCherry_hND6_.rlog.tsv md5sum: 1077cf03a8c6a155932eaaed7415b74c - path: output/tsv/test.csv md5sum: f8e51c79c9add0d07eb46aba6a09d33c @@ -117,21 +117,21 @@ - deseq2 - deseq2/differential files: - - path: output/deseq2/treatment-mCherry-hND6-sample_number.deseq2.results.tsv + - path: output/deseq2/treatment_mCherry_hND6_sample_number.deseq2.results.tsv md5sum: 86f0312a4691dfb4d7c15643059d8fb8 - - path: output/deseq2/treatment-mCherry-hND6-sample_number.deseq2.sizefactors.tsv + - path: output/deseq2/treatment_mCherry_hND6_sample_number.deseq2.sizefactors.tsv md5sum: 6332f21889ecac387bb12eeb04f23849 - - path: output/deseq2/treatment-mCherry-hND6-sample_number.normalised_counts.tsv + - path: output/deseq2/treatment_mCherry_hND6_sample_number.normalised_counts.tsv md5sum: 827cdf01f366d72d6e4b500e9862ba74 - - path: output/deseq2/treatment-mCherry-hND6-sample_number.vst.tsv + - path: output/deseq2/treatment_mCherry_hND6_sample_number.vst.tsv md5sum: 0960df48c0116a626289960284148fbb - - path: output/deseq2/treatment-mCherry-hND6.deseq2.results.tsv + - path: output/deseq2/treatment_mCherry_hND6_.deseq2.results.tsv md5sum: 4034522732d975951c79731acc1c9731 - - path: output/deseq2/treatment-mCherry-hND6.deseq2.sizefactors.tsv + - path: output/deseq2/treatment_mCherry_hND6_.deseq2.sizefactors.tsv md5sum: 6332f21889ecac387bb12eeb04f23849 - - path: output/deseq2/treatment-mCherry-hND6.normalised_counts.tsv + - path: output/deseq2/treatment_mCherry_hND6_.normalised_counts.tsv md5sum: 827cdf01f366d72d6e4b500e9862ba74 - - path: output/deseq2/treatment-mCherry-hND6.vst.tsv + - path: output/deseq2/treatment_mCherry_hND6_.vst.tsv md5sum: 0960df48c0116a626289960284148fbb - name: deseq2 differential test_deseq2_differential_subset_to_contrast @@ -140,21 +140,21 @@ - deseq2 - deseq2/differential files: - - path: output/deseq2/treatment-mCherry-hND6-sample_number.deseq2.results.tsv + - path: output/deseq2/treatment_mCherry_hND6_sample_number.deseq2.results.tsv md5sum: 86f0312a4691dfb4d7c15643059d8fb8 - - path: output/deseq2/treatment-mCherry-hND6-sample_number.deseq2.sizefactors.tsv + - path: output/deseq2/treatment_mCherry_hND6_sample_number.deseq2.sizefactors.tsv md5sum: 6332f21889ecac387bb12eeb04f23849 - - path: output/deseq2/treatment-mCherry-hND6-sample_number.normalised_counts.tsv + - path: output/deseq2/treatment_mCherry_hND6_sample_number.normalised_counts.tsv md5sum: 827cdf01f366d72d6e4b500e9862ba74 - - path: output/deseq2/treatment-mCherry-hND6-sample_number.rlog.tsv + - path: output/deseq2/treatment_mCherry_hND6_sample_number.rlog.tsv md5sum: 1077cf03a8c6a155932eaaed7415b74c - - path: output/deseq2/treatment-mCherry-hND6.deseq2.results.tsv + - path: output/deseq2/treatment_mCherry_hND6_.deseq2.results.tsv md5sum: 4034522732d975951c79731acc1c9731 - - path: output/deseq2/treatment-mCherry-hND6.deseq2.sizefactors.tsv + - path: output/deseq2/treatment_mCherry_hND6_.deseq2.sizefactors.tsv md5sum: 6332f21889ecac387bb12eeb04f23849 - - path: output/deseq2/treatment-mCherry-hND6.normalised_counts.tsv + - path: output/deseq2/treatment_mCherry_hND6_.normalised_counts.tsv md5sum: 827cdf01f366d72d6e4b500e9862ba74 - - path: output/deseq2/treatment-mCherry-hND6.rlog.tsv + - path: output/deseq2/treatment_mCherry_hND6_.rlog.tsv md5sum: 1077cf03a8c6a155932eaaed7415b74c - name: deseq2 differential test_deseq2_differential_exclude_samples @@ -163,19 +163,19 @@ - deseq2 - deseq2/differential files: - - path: output/deseq2/treatment-mCherry-hND6-sample_number.deseq2.results.tsv + - path: output/deseq2/treatment_mCherry_hND6_sample_number.deseq2.results.tsv contains: ["ENSMUSG00000023978\t396.73852567\t4.843056\t1.18395002\t2.130893e-06\t7.938188e-05"] - - path: output/deseq2/treatment-mCherry-hND6-sample_number.deseq2.sizefactors.tsv + - path: output/deseq2/treatment_mCherry_hND6_sample_number.deseq2.sizefactors.tsv md5sum: 87d6d634ffea2d7a9df9f9bae91b4d90 - - path: output/deseq2/treatment-mCherry-hND6-sample_number.normalised_counts.tsv + - path: output/deseq2/treatment_mCherry_hND6_sample_number.normalised_counts.tsv md5sum: 32c6fb71cc4b296c66e06f6eed96428b - - path: output/deseq2/treatment-mCherry-hND6-sample_number.rlog.tsv + - path: output/deseq2/treatment_mCherry_hND6_sample_number.rlog.tsv md5sum: 1ed46435eed7cda5d7fcb91b2b5d4429 - - path: output/deseq2/treatment-mCherry-hND6.deseq2.results.tsv + - path: output/deseq2/treatment_mCherry_hND6_.deseq2.results.tsv contains: ["ENSMUSG00000023978\t396.73852567\t7.724976\t1.52788385\t4.774373e-08\t5.231349e-06"] - - path: output/deseq2/treatment-mCherry-hND6.deseq2.sizefactors.tsv + - path: output/deseq2/treatment_mCherry_hND6_.deseq2.sizefactors.tsv md5sum: 87d6d634ffea2d7a9df9f9bae91b4d90 - - path: output/deseq2/treatment-mCherry-hND6.normalised_counts.tsv + - path: output/deseq2/treatment_mCherry_hND6_.normalised_counts.tsv md5sum: 32c6fb71cc4b296c66e06f6eed96428b - - path: output/deseq2/treatment-mCherry-hND6.rlog.tsv + - path: output/deseq2/treatment_mCherry_hND6_.rlog.tsv md5sum: 1ed46435eed7cda5d7fcb91b2b5d4429 diff --git a/tests/modules/nf-core/limma/differential/main.nf b/tests/modules/nf-core/limma/differential/main.nf index 9b83d5c24ae..c1e097b0e55 100644 --- a/tests/modules/nf-core/limma/differential/main.nf +++ b/tests/modules/nf-core/limma/differential/main.nf @@ -31,7 +31,7 @@ workflow test_limma_differential { ch_intensities = ch_samplesheet .join(AFFY_JUSTRMA.out.expression) - ch_contrasts = Channel.of(['variable': 'diagnosis', 'reference': 'normal', 'target': 'uremia']) + ch_contrasts = Channel.of(['id': 'diagnosis_normal_uremia', 'variable': 'diagnosis', 'reference': 'normal', 'target': 'uremia']) .map{ tuple(it, it.variable, it.reference, it.target) } @@ -67,7 +67,7 @@ workflow test_limma_differential_subset_to_contrast { ch_intensities = ch_samplesheet .join(AFFY_JUSTRMA.out.expression) - ch_contrasts = Channel.of(['variable': 'diagnosis', 'reference': 'normal', 'target': 'uremia']) + ch_contrasts = Channel.of(['id': 'diagnosis_normal_uremia', 'variable': 'diagnosis', 'reference': 'normal', 'target': 'uremia']) .map{ tuple(it, it.variable, it.reference, it.target) } @@ -104,7 +104,7 @@ workflow test_limma_differential_exclude_samples { ch_intensities = ch_samplesheet .join(AFFY_JUSTRMA.out.expression) - ch_contrasts = Channel.of(['variable': 'diagnosis', 'reference': 'normal', 'target': 'uremia']) + ch_contrasts = Channel.of(['id': 'diagnosis_normal_uremia', 'variable': 'diagnosis', 'reference': 'normal', 'target': 'uremia']) .map{ tuple(it, it.variable, it.reference, it.target) } diff --git a/tests/modules/nf-core/limma/differential/test.yml b/tests/modules/nf-core/limma/differential/test.yml index 6c75a8e8aae..61c09cae720 100644 --- a/tests/modules/nf-core/limma/differential/test.yml +++ b/tests/modules/nf-core/limma/differential/test.yml @@ -4,11 +4,11 @@ - limma - limma/differential files: - - path: output/limma/diagnosis-normal-uremia.MArrayLM.limma.rds - - path: output/limma/diagnosis-normal-uremia.R_sessionInfo.log + - path: output/limma/diagnosis_normal_uremia.MArrayLM.limma.rds + - path: output/limma/diagnosis_normal_uremia.R_sessionInfo.log contains: ["limma_3.54.0"] - - path: output/limma/diagnosis-normal-uremia.limma.mean_difference.png - - path: output/limma/diagnosis-normal-uremia.limma.results.tsv + - path: output/limma/diagnosis_normal_uremia.limma.mean_difference.png + - path: output/limma/diagnosis_normal_uremia.limma.results.tsv contains: ["1007_s_at\t-0.2775254", "1053_at\t-0.071547786"] - path: output/limma/versions.yml @@ -18,11 +18,11 @@ - limma - limma/differential files: - - path: output/limma/diagnosis-normal-uremia.MArrayLM.limma.rds - - path: output/limma/diagnosis-normal-uremia.R_sessionInfo.log + - path: output/limma/diagnosis_normal_uremia.MArrayLM.limma.rds + - path: output/limma/diagnosis_normal_uremia.R_sessionInfo.log contains: ["limma_3.54.0"] - - path: output/limma/diagnosis-normal-uremia.limma.mean_difference.png - - path: output/limma/diagnosis-normal-uremia.limma.results.tsv + - path: output/limma/diagnosis_normal_uremia.limma.mean_difference.png + - path: output/limma/diagnosis_normal_uremia.limma.results.tsv contains: ["1007_s_at\t-0.2775254", "1053_at\t-0.071547786"] - path: output/limma/versions.yml @@ -32,10 +32,10 @@ - limma - limma/differential files: - - path: output/limma/diagnosis-normal-uremia.MArrayLM.limma.rds - - path: output/limma/diagnosis-normal-uremia.R_sessionInfo.log + - path: output/limma/diagnosis_normal_uremia.MArrayLM.limma.rds + - path: output/limma/diagnosis_normal_uremia.R_sessionInfo.log contains: ["limma_3.54.0"] - - path: output/limma/diagnosis-normal-uremia.limma.mean_difference.png - - path: output/limma/diagnosis-normal-uremia.limma.results.tsv + - path: output/limma/diagnosis_normal_uremia.limma.mean_difference.png + - path: output/limma/diagnosis_normal_uremia.limma.results.tsv contains: ["1007_s_at\t-0.4778282", "1053_at\t-0.08958278"] - path: output/limma/versions.yml