Update paramsValidator for FASTQ split

lina-kim · May 24, 2024 · 9aa412e · 9aa412e
1 parent a36e7b1
commit 9aa412e
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Showing 4 changed files with 10 additions and 3 deletions.
diff --git a/docs/readme_docs.md b/docs/readme_docs.md
@@ -48,7 +48,7 @@ Required if running Cutadapt:
 ## Optional user-input parameters
 
 Used for initial FASTQ processing in scope `params.fastq_split`:
-* `enabled`: default `null`, determines whether samples will be processed as a batch or individually; either `"True"` or `"False"`
+* `enabled`: default `true`, determines whether samples will be processed as a batch or individually; either `true` or `false`
 * `method`: default `"sample"`, represents method by which to split input FASTQ file manifest; either `"sample"` or an integer representing the number of split artifacts for processing 
 * `suffix`: default `"_split.tsv"`, suffix for split FASTQ manifest files used as intermediates
 

diff --git a/lib/paramsValidator.nf b/lib/paramsValidator.nf
@@ -217,6 +217,13 @@ def validateParams(params) {
 	assertParam(params.fastqc_release, [String], null, "fastqc_release must be a String")
 	assertParam(params.multiqc_container, [String], null, "multiqc_container must be a String")
 
+	/////////////////////////////////////////////////
+	// Validation for pre-denoise split parameters //
+	/////////////////////////////////////////////////
+	def fastq_split = params.fastq_split
+	assertParam(fastq_split.enabled, [Boolean], [true, false], "fastq_split.enabled must be true or false")
+	assertParam(fastq_split.suffix, [String], null, "fastq_split.suffix must be a String")
+	assertParam(fastq_split.method, [Integer, String], [{ it instanceof Integer && it > 0 }, "sample"], "fastq_split.method must be 1) an integer greater than 0, representing the number of split artifacts to create; or 2) the string 'sample', representing individual artifacts per sample pre-denoising.")
 }
 
 def validateTsvFile(filePath) {

diff --git a/workflows/download.nf b/workflows/download.nf
@@ -133,7 +133,7 @@ workflow DOWNLOAD {
     if (params.generate_input) {
         ch_inp_ids = Channel.fromPath ( "${params.inp_id_file}", checkIfExists: true )
                         .map { [0, it] }
-        if (params.fastq_split.enabled == "True") {
+        if (params.fastq_split.enabled) {
             SPLIT_FASTQ_MANIFEST ( ch_inp_ids )
             manifest_suffix = ~/${params.fastq_split.suffix}/
             ch_acc_ids = SPLIT_FASTQ_MANIFEST.out

diff --git a/workflows/import.nf b/workflows/import.nf
@@ -136,7 +136,7 @@ workflow IMPORT {
                                         .map { [0, it] }
 
         // Use local FASTQ files
-        if (params.fastq_split.enabled == "True") {
+        if (params.fastq_split.enabled) {
             SPLIT_FASTQ_MANIFEST ( ch_fastq_manifest )
             manifest_suffix = ~/${params.fastq_split.suffix}/
             ch_acc_ids = SPLIT_FASTQ_MANIFEST.out