merge fix

kedhammar · kedhammar · commit a5951302f2b7 · 2024-10-28T13:30:37.000Z
diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -74,6 +74,7 @@ workflow PIPELINE_INITIALISATION {
 
     Channel
         .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
+        .toList()
         .flatMap { it.withIndex().collect {  entry, idx -> entry + "${idx+1}" } }
         .map {
             meta, fastq_1, fastq_2, idx ->
@@ -94,8 +95,8 @@ workflow PIPELINE_INITIALISATION {
                 }
         }
         .groupTuple()
-        .map { samplesheet ->
-            validateInputSamplesheet(samplesheet)
+        .map {
+            validateInputSamplesheet(it) // Applies additional group validation checks that schema_input.json cannot do.
         }
         .transpose() // Replace the map below
         // .map {

Original file line number	Diff line number	Diff line change
`@@ -74,6 +74,7 @@ workflow PIPELINE_INITIALISATION {`
`74`	`74`
`75`	`75`	`Channel`
`76`	`76`	`.fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))`
	`77`	`+ .toList()`
`77`	`78`	`.flatMap { it.withIndex().collect { entry, idx -> entry + "${idx+1}" } }`
`78`	`79`	`.map {`
`79`	`80`	`meta, fastq_1, fastq_2, idx ->`
`@@ -94,8 +95,8 @@ workflow PIPELINE_INITIALISATION {`
`94`	`95`	`}`
`95`	`96`	`}`
`96`	`97`	`.groupTuple()`
`97`		`- .map { samplesheet ->`
`98`		`- validateInputSamplesheet(samplesheet)`
	`98`	`+ .map {`
	`99`	`+ validateInputSamplesheet(it) // Applies additional group validation checks that schema_input.json cannot do.`
`99`	`100`	`}`
`100`	`101`	`.transpose() // Replace the map below`
`101`	`102`	`// .map {`