Replace publishDir with workflow output definition

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

main.nf

@@ -62,3 +62,16 @@ workflow {
 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' {
+    path '.'
+  }
+
+  'multiqc' {
+    path '.'
+  }
+}

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:
     """