Replace publishDir with workflow output definition

main.nf

@@ -25,6 +25,8 @@
  */
 nextflow.enable.dsl = 2
 
+nextflow.preview.output = true
+
 /*
  * Default pipeline parameters. They can be overriden on the command line eg.
  * given `params.foo` specify on the run command line `--foo some_value`.
@@ -56,9 +58,12 @@ workflow {
   MULTIQC( RNASEQ.out, params.multiqc )
 }
 
-/* 
- * completion handler
- */
-workflow.onComplete {
-	log.info ( workflow.success ? "\nDone! Open the following report in your browser --> $params.outdir/multiqc_report.html\n" : "Oops .. something went wrong" )
+output {
+  directory params.outdir
+  mode 'copy'
+  fastqc {
+    index {
+      path 'index.csv'
+    }
+  }
 }

modules/fastqc/main.nf

@@ -1,15 +1,16 @@
-params.outdir = 'results'
 
 process FASTQC {
     tag "FASTQC on $sample_id"
     conda 'fastqc=0.12.1'
-    publishDir params.outdir, mode:'copy'
 
     input:
     tuple val(sample_id), path(reads)
 
     output:
-    path "fastqc_${sample_id}_logs" 
+    path "fastqc_${sample_id}_logs", emit: logs
+
+    publish:
+    logs >> 'fastqc'
 
     script:
     """

modules/multiqc/main.nf

@@ -1,15 +1,16 @@
-params.outdir = 'results'
 
 process MULTIQC {
     conda 'multiqc=1.17'
-    publishDir params.outdir, mode:'copy'
 
     input:
     path('*') 
     path(config) 
 
     output:
-    path('multiqc_report.html')
+    path('multiqc_report.html'), emit: report
+
+    publish:
+    report >> 'multiqc'
 
     script:
     """

modules/rnaseq.nf

@@ -16,4 +16,4 @@ workflow RNASEQ {
 
   emit: 
      QUANT.out | concat(FASTQC.out) | collect
-}
+}