R differential modules control over output prefixes (nf-core#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
JPejovicApis · Oct 10, 2023 · f288d50 · f288d50
1 parent fb809db
commit f288d50
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Showing 8 changed files with 95 additions and 101 deletions.
diff --git 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
@@ -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
@@ -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
 )
@@ -375,15 +372,15 @@ 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 = '.'))
 
 ################################################
 ################################################
 ## R SESSION INFO                             ##
 ################################################
 ################################################
 
-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
@@ -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
@@ -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