From bfbbc6680552674b255f30bc32e5b433dc8d5b39 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <pininforthefjords@gmail.com>
Date: Sun, 23 Jul 2023 21:57:31 +0100
Subject: [PATCH 01/12] R differential modules control over output prefixes

---
 .../deseq2/differential/templates/deseq_de.R  | 21 ++++++++-----------
 .../limma/differential/templates/limma_de.R   | 15 ++++++-------
 2 files changed, 15 insertions(+), 21 deletions(-)

diff --git a/modules/nf-core/deseq2/differential/templates/deseq_de.R b/modules/nf-core/deseq2/differential/templates/deseq_de.R
index f1fcd847349..d3ad0177684 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 = '$task.ext.prefix',
     count_file = '$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..b7e73c95cf1 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 = '$task.ext.prefix',
     count_file = '$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()
 

From a4e57f600d023b7433f1948a0589431dfbaa3982 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <pininforthefjords@gmail.com>
Date: Sun, 23 Jul 2023 22:25:31 +0100
Subject: [PATCH 02/12] Set differential module prefixes

---
 modules/nf-core/deseq2/differential/main.nf | 1 +
 modules/nf-core/limma/differential/main.nf  | 1 +
 2 files changed, 2 insertions(+)

diff --git a/modules/nf-core/deseq2/differential/main.nf b/modules/nf-core/deseq2/differential/main.nf
index bad536b2e01..cdc9ca9f0ce 100644
--- a/modules/nf-core/deseq2/differential/main.nf
+++ b/modules/nf-core/deseq2/differential/main.nf
@@ -27,5 +27,6 @@ process DESEQ2_DIFFERENTIAL {
     task.ext.when == null || task.ext.when
 
     script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
     template 'deseq_de.R'
 }
diff --git a/modules/nf-core/limma/differential/main.nf b/modules/nf-core/limma/differential/main.nf
index 364c5a13756..aa9d39b844c 100644
--- a/modules/nf-core/limma/differential/main.nf
+++ b/modules/nf-core/limma/differential/main.nf
@@ -22,5 +22,6 @@ process LIMMA_DIFFERENTIAL {
     task.ext.when == null || task.ext.when
 
     script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
     template 'limma_de.R'
 }

From 185e2718b44db3195ca807caa89697c77548e135 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <pininforthefjords@gmail.com>
Date: Sun, 23 Jul 2023 22:33:27 +0100
Subject: [PATCH 03/12] Actually we need to do prefix handling within the
 template

---
 modules/nf-core/deseq2/differential/main.nf              | 1 -
 modules/nf-core/deseq2/differential/templates/deseq_de.R | 2 +-
 modules/nf-core/limma/differential/main.nf               | 1 -
 modules/nf-core/limma/differential/templates/limma_de.R  | 2 +-
 4 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/deseq2/differential/main.nf b/modules/nf-core/deseq2/differential/main.nf
index cdc9ca9f0ce..bad536b2e01 100644
--- a/modules/nf-core/deseq2/differential/main.nf
+++ b/modules/nf-core/deseq2/differential/main.nf
@@ -27,6 +27,5 @@ process DESEQ2_DIFFERENTIAL {
     task.ext.when == null || task.ext.when
 
     script:
-    def prefix = task.ext.prefix ?: "${meta.id}"
     template 'deseq_de.R'
 }
diff --git a/modules/nf-core/deseq2/differential/templates/deseq_de.R b/modules/nf-core/deseq2/differential/templates/deseq_de.R
index d3ad0177684..681031b1315 100755
--- a/modules/nf-core/deseq2/differential/templates/deseq_de.R
+++ b/modules/nf-core/deseq2/differential/templates/deseq_de.R
@@ -93,7 +93,7 @@ round_dataframe_columns <- function(df, columns = NULL, digits = 8){
 # Set defaults and classes
 
 opt <- list(
-    output_prefix = '$task.ext.prefix',
+    output_prefix = ifelse('$task.ext.prefix' == 'null', '$meta.id', '$task.ext.prefix')
     count_file = '$counts',
     sample_file = '$samplesheet',
     contrast_variable = '$contrast_variable',
diff --git a/modules/nf-core/limma/differential/main.nf b/modules/nf-core/limma/differential/main.nf
index aa9d39b844c..364c5a13756 100644
--- a/modules/nf-core/limma/differential/main.nf
+++ b/modules/nf-core/limma/differential/main.nf
@@ -22,6 +22,5 @@ process LIMMA_DIFFERENTIAL {
     task.ext.when == null || task.ext.when
 
     script:
-    def prefix = task.ext.prefix ?: "${meta.id}"
     template 'limma_de.R'
 }
diff --git a/modules/nf-core/limma/differential/templates/limma_de.R b/modules/nf-core/limma/differential/templates/limma_de.R
index b7e73c95cf1..2af47bbf80c 100755
--- a/modules/nf-core/limma/differential/templates/limma_de.R
+++ b/modules/nf-core/limma/differential/templates/limma_de.R
@@ -65,7 +65,7 @@ read_delim_flexible <- function(file, header = TRUE, row.names = NULL, check.nam
 # Set defaults and classes
 
 opt <- list(
-    output_prefix = '$task.ext.prefix',
+    output_prefix = ifelse('$task.ext.prefix' == 'null', '$meta.id', '$task.ext.prefix')
     count_file = '$intensities',
     sample_file = '$samplesheet',
     contrast_variable = '$contrast_variable',

From 13e2b6087c11b542b787499b14f273239b032439 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <pininforthefjords@gmail.com>
Date: Sun, 23 Jul 2023 22:39:05 +0100
Subject: [PATCH 04/12] Set differential module prefixes

---
 modules/nf-core/deseq2/differential/templates/deseq_de.R | 2 +-
 modules/nf-core/limma/differential/templates/limma_de.R  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/deseq2/differential/templates/deseq_de.R b/modules/nf-core/deseq2/differential/templates/deseq_de.R
index 681031b1315..0c7ea82d5bc 100755
--- a/modules/nf-core/deseq2/differential/templates/deseq_de.R
+++ b/modules/nf-core/deseq2/differential/templates/deseq_de.R
@@ -93,7 +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', '$task.ext.prefix')
+    output_prefix = ifelse('$task.ext.prefix' == 'null', '$meta.id', '$task.ext.prefix'),
     count_file = '$counts',
     sample_file = '$samplesheet',
     contrast_variable = '$contrast_variable',
diff --git a/modules/nf-core/limma/differential/templates/limma_de.R b/modules/nf-core/limma/differential/templates/limma_de.R
index 2af47bbf80c..5a80eb22923 100755
--- a/modules/nf-core/limma/differential/templates/limma_de.R
+++ b/modules/nf-core/limma/differential/templates/limma_de.R
@@ -65,7 +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', '$task.ext.prefix')
+    output_prefix = ifelse('$task.ext.prefix' == 'null', '$meta.id', '$task.ext.prefix'),
     count_file = '$intensities',
     sample_file = '$samplesheet',
     contrast_variable = '$contrast_variable',

From 947cba0c9d2514424be3cbdaeed58546bf597419 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <pininforthefjords@gmail.com>
Date: Sun, 23 Jul 2023 22:49:09 +0100
Subject: [PATCH 05/12] Fix test files for new prefix specification

---
 .../nf-core/deseq2/differential/test.yml      | 120 +++++++++---------
 .../nf-core/limma/differential/test.yml       |  24 ++--
 2 files changed, 72 insertions(+), 72 deletions(-)

diff --git a/tests/modules/nf-core/deseq2/differential/test.yml b/tests/modules/nf-core/deseq2/differential/test.yml
index 3fd1f45150e..bcd45c62373 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/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

From 0c75a420cf5a7e1f9aeb6274e8027222c2a752ad Mon Sep 17 00:00:00 2001
From: Jonathan Manning <pininforthefjords@gmail.com>
Date: Sun, 23 Jul 2023 23:02:23 +0100
Subject: [PATCH 06/12] Add meta to limma test

---
 tests/modules/nf-core/limma/differential/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/modules/nf-core/limma/differential/main.nf b/tests/modules/nf-core/limma/differential/main.nf
index 9b83d5c24ae..3aa8a3ffd21 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)
         }

From 9957f7a5657e49eba3c6d1ec8d05a20d8c6c43af Mon Sep 17 00:00:00 2001
From: Jonathan Manning <pininforthefjords@gmail.com>
Date: Sun, 23 Jul 2023 23:06:23 +0100
Subject: [PATCH 07/12] Fix DESeq2 tests

---
 .../nf-core/deseq2/differential/test.yml      | 64 +++++++++----------
 1 file changed, 32 insertions(+), 32 deletions(-)

diff --git a/tests/modules/nf-core/deseq2/differential/test.yml b/tests/modules/nf-core/deseq2/differential/test.yml
index bcd45c62373..e878d56e20c 100644
--- a/tests/modules/nf-core/deseq2/differential/test.yml
+++ b/tests/modules/nf-core/deseq2/differential/test.yml
@@ -12,13 +12,13 @@
       md5sum: 827cdf01f366d72d6e4b500e9862ba74
     - 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
@@ -50,13 +50,13 @@
       md5sum: 1c9c7ee4ca90ff0d91ae16dbfd64fdc9
     - 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
@@ -75,13 +75,13 @@
       md5sum: bb916c41f91b2ddcc9607619a023ef44
     - 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
@@ -100,13 +100,13 @@
       md5sum: 827cdf01f366d72d6e4b500e9862ba74
     - 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
@@ -125,13 +125,13 @@
       md5sum: 827cdf01f366d72d6e4b500e9862ba74
     - 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
@@ -148,13 +148,13 @@
       md5sum: 827cdf01f366d72d6e4b500e9862ba74
     - 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
@@ -171,11 +171,11 @@
       md5sum: 32c6fb71cc4b296c66e06f6eed96428b
     - 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

From fc6a071e19631e764a0e36a199a73708be28dc03 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <pininforthefjords@gmail.com>
Date: Mon, 24 Jul 2023 09:07:02 +0100
Subject: [PATCH 08/12] fix remaining tests for limma

---
 tests/modules/nf-core/limma/differential/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/modules/nf-core/limma/differential/main.nf b/tests/modules/nf-core/limma/differential/main.nf
index 3aa8a3ffd21..c1e097b0e55 100644
--- a/tests/modules/nf-core/limma/differential/main.nf
+++ b/tests/modules/nf-core/limma/differential/main.nf
@@ -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)
         }

From 4ed42f723e7c3f2b83f3211d6f1243dc63ca8ae3 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <pininforthefjords@gmail.com>
Date: Mon, 24 Jul 2023 13:23:45 +0100
Subject: [PATCH 09/12] Update grep to fix broken solve

---
 modules/nf-core/untar/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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' }"

From 64850a41b511611add742f39d20de7c7ec71f18a Mon Sep 17 00:00:00 2001
From: Jonathan Manning <pininforthefjords@gmail.com>
Date: Mon, 24 Jul 2023 14:12:09 +0100
Subject: [PATCH 10/12] Try bumping affy

---
 modules/nf-core/affy/justrma/main.nf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/nf-core/affy/justrma/main.nf b/modules/nf-core/affy/justrma/main.nf
index 40ebcbf1847..dff0709f6f0 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_0':
+        'biocontainers/bioconductor-affy:1.78.0--r43ha9d7317_0' }"
 
     input:
     tuple val(meta), path(samplesheet), path(celfiles_dir)

From 0e45520a9d3218580192c7caea12ef96bf6b8ed6 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <pininforthefjords@gmail.com>
Date: Mon, 24 Jul 2023 19:24:02 +0100
Subject: [PATCH 11/12] Use new build

---
 modules/nf-core/affy/justrma/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/affy/justrma/main.nf b/modules/nf-core/affy/justrma/main.nf
index dff0709f6f0..d0da712948f 100644
--- a/modules/nf-core/affy/justrma/main.nf
+++ b/modules/nf-core/affy/justrma/main.nf
@@ -4,8 +4,8 @@ process AFFY_JUSTRMA {
 
     conda "bioconda::bioconductor-affy=1.78.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-affy:1.78.0--r43ha9d7317_0':
-        'biocontainers/bioconductor-affy:1.78.0--r43ha9d7317_0' }"
+        '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)

From 67dc6a1bec2ef734bf2ea5628f60fa0b9a24e933 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <pininforthefjords@gmail.com>
Date: Mon, 24 Jul 2023 21:27:14 +0100
Subject: [PATCH 12/12] update md5sum for annotation

---
 tests/modules/nf-core/affy/justrma/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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