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R differential modules control over output prefixes #3664

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merged 13 commits into from
Jul 25, 2023
Merged

R differential modules control over output prefixes #3664

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bfbbc66
R differential modules control over output prefixes
pinin4fjords Jul 23, 2023
a4e57f6
Set differential module prefixes
pinin4fjords Jul 23, 2023
185e271
Actually we need to do prefix handling within the template
pinin4fjords Jul 23, 2023
13e2b60
Set differential module prefixes
pinin4fjords Jul 23, 2023
947cba0
Fix test files for new prefix specification
pinin4fjords Jul 23, 2023
0c75a42
Add meta to limma test
pinin4fjords Jul 23, 2023
9957f7a
Fix DESeq2 tests
pinin4fjords Jul 23, 2023
fc6a071
fix remaining tests for limma
pinin4fjords Jul 24, 2023
4ed42f7
Update grep to fix broken solve
pinin4fjords Jul 24, 2023
64850a4
Try bumping affy
pinin4fjords Jul 24, 2023
0e45520
Use new build
pinin4fjords Jul 24, 2023
67dc6a1
update md5sum for annotation
pinin4fjords Jul 24, 2023
98a972e
Merge branch 'master' into differential_module_prefixes
Jul 24, 2023
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6 changes: 3 additions & 3 deletions modules/nf-core/affy/justrma/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down
21 changes: 9 additions & 12 deletions modules/nf-core/deseq2/differential/templates/deseq_de.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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',
Expand Down Expand Up @@ -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){
Expand Down Expand Up @@ -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 = "")
Expand All @@ -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',
Expand All @@ -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
)
Expand All @@ -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

Expand All @@ -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',
Expand All @@ -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',
Expand All @@ -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',
Expand All @@ -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()

Expand Down
15 changes: 6 additions & 9 deletions modules/nf-core/limma/differential/templates/limma_de.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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',
Expand Down Expand Up @@ -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){
Expand Down Expand Up @@ -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 = "")
Expand All @@ -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',
Expand All @@ -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
)
Expand All @@ -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()

Expand Down
2 changes: 1 addition & 1 deletion modules/nf-core/untar/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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' }"
Expand Down
2 changes: 1 addition & 1 deletion tests/modules/nf-core/affy/justrma/test.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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