feat: handle boolean parameters from groovy to R

Author: kelly-sovacool

main.nf

@@ -18,6 +18,7 @@ counts       : ${params.counts}
 .stripIndent()
 
 include { create_multiOmicDataSet_from_files } from './modules/local/mosuite/create_multiOmicDataSet_from_files/'
+include { clean_raw_counts } from './modules/local/mosuite/clean_raw_counts/'
 
 // workflow.onComplete {
 //     if (!workflow.stubRun && !workflow.commandLine.contains('-preview')) {
@@ -32,5 +33,7 @@ workflow {
     ch_input = Channel.fromPath(file(params.samplesheet, checkIfExists: true))
         .combine(Channel.fromPath(file(params.counts, checkIfExists: true)))
 
-    ch_input | create_multiOmicDataSet_from_files
+    ch_moo = ch_input |
+        create_multiOmicDataSet_from_files
+    clean_raw_counts(ch_moo, [ params.aggregate_rows_with_duplicate_gene_names, params.cleanup_column_names, params.split_gene_name ])
 }

modules/local/mosuite/clean_raw_counts/main.nf

@@ -0,0 +1,32 @@
+process clean_raw_counts {
+    container "${params.container}"
+
+    input:
+    path(moo)
+    tuple val(aggregate_rows_with_duplicate_gene_names), val(cleanup_column_names), val(split_gene_name)
+
+    output:
+    path("moo_clean.rds"), emit: 'moo'
+    path("figures/"), emit: figures
+
+    script:
+    """
+    #!/usr/bin/env Rscript
+
+    options(MOO_SAVE_PLOTS = TRUE)
+    library(MOSuite)
+
+    true <- TRUE
+    false <- FALSE
+    null <- NULL
+
+    moo <- readr::read_rds("$moo") |>
+        clean_raw_counts(
+            aggregate_rows_with_duplicate_gene_names = $aggregate_rows_with_duplicate_gene_names,
+            cleanup_column_names = $cleanup_column_names,
+            split_gene_name = $split_gene_name
+            )
+
+    readr::write_rds(moo, "moo_clean.rds")
+    """
+}

modules/local/mosuite/create_multiOmicDataSet_from_files/main.nf

@@ -5,7 +5,7 @@ process create_multiOmicDataSet_from_files {
     tuple path(samplesheet), path(counts)
 
     output:
-    path("moo*.rds")
+    path("moo*.rds"), emit: moo
 
     script:
     """

nextflow.config

@@ -5,6 +5,11 @@ params {
     samplesheet = null
     counts = null
 
+    // clean_raw_counts
+    aggregate_rows_with_duplicate_gene_names = true
+    cleanup_column_names = true
+    split_gene_name = true
+
     // Boilerplate options
     outputDir = 'results'
     tracedir = "${params.outputDir}/pipeline_info"