Revert let to def

Signed-off-by: Ben Sherman <[email protected]>

Author: bentsherman

main.nf

@@ -50,14 +50,14 @@ workflow {
     outdir       : ${workflow.outputDir}
     """.stripIndent()
 
-  let (index, samples) = params.reads
+  def (index, samples) = params.reads
     |> Channel.fromFilePairs( checkIfExists: true )         // Channel<(String,List<Path>)>
     |> map { (id, reads) ->
       new FastqPair(id, reads[0], reads[1])
     }                                                       // Channel<FastqPair>
     |> RNASEQ( file(params.transcriptome) )                 // NamedTuple(index: Path, samples: Channel<Sample>)
 
-  let summary = samples
+  def summary = samples
     |> flatMap { s -> [ s.fastqc, s.quant ] }               // Channel<Path>
     |> collect                                              // Bag<Path> (future)
     |> MULTIQC( file(params.multiqc) )                      // Path (future)

modules/rnaseq.nf

@@ -14,9 +14,9 @@ workflow RNASEQ {
 
   pairs                       // Channel<FastqPair>
     |> map { pair ->
-      let (id, fastq_1, fastq_2) = (pair.id, pair.fastq_1, pair.fastq_2)
-      let fastqc = FASTQC(id, fastq_1, fastq_2)
-      let quant = QUANT(index, id, fastq_1, fastq_2)
+      def (id, fastq_1, fastq_2) = (pair.id, pair.fastq_1, pair.fastq_2)
+      def fastqc = FASTQC(id, fastq_1, fastq_2)
+      def quant = QUANT(index, id, fastq_1, fastq_2)
       new Sample(id, fastqc, quant)
     }                         // Channel<Sample>
     |> set { samples }        // Channel<Sample>