Fix variable definiton order

workflow/main.nf

@@ -27,25 +27,6 @@ if (params.kitVersion == "3GEXv3" && params.version == '2.1.1') {
   System.exit(32)	
 }
 
-// Define variables from input
-name = params.name
-designLocation = Channel
-  .fromPath(params.designFile)
-  .ifEmpty { exit 1, "design file not found: ${params.designFile}" }
-fastqList = Channel
-  .fromPath(params.fastq)
-  .flatten()
-  .map { file -> [ file.getFileName().toString(), file.toString() ].join("\t") }
-  .collectFile(name: 'fileList.tsv', newLine: true)
-refLocation = Channel
-  .fromPath(params.genomeLocationFull)
-  .ifEmpty { exit 1, "referene not found: ${params.genome}" }
-expectCells = params.expectCells
-forceCells = params.forceCells
-chemistryParam = params.chemistryParam
-version = params.version
-outDir = params.outDir
-
 // Define variables if astrocyte (or from config)
 if (params.astrocyte) {
   print("Running under astrocyte")
@@ -67,6 +48,25 @@ if (params.astrocyte) {
 }
 params.genomeLocationFull = params.genomeLocation+params.genome
 
+// Define variables from input
+name = params.name
+designLocation = Channel
+  .fromPath(params.designFile)
+  .ifEmpty { exit 1, "design file not found: ${params.designFile}" }
+fastqList = Channel
+  .fromPath(params.fastq)
+  .flatten()
+  .map { file -> [ file.getFileName().toString(), file.toString() ].join("\t") }
+  .collectFile(name: 'fileList.tsv', newLine: true)
+refLocation = Channel
+  .fromPath(params.genomeLocationFull)
+  .ifEmpty { exit 1, "referene not found: ${params.genome}" }
+expectCells = params.expectCells
+forceCells = params.forceCells
+chemistryParam = params.chemistryParam
+version = params.version
+outDir = params.outDir
+
 // Define constant variables
 multiqcConf = "${baseDir}/conf/multiqc_config.yaml"
 references = "${baseDir}/../docs/references.md"