Workflow outputs (first preview)

main.nf

@@ -5,6 +5,8 @@
  */
 
 
+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`.
@@ -37,3 +39,13 @@ log.info """\
   RNASEQ( params.transcriptome, read_pairs_ch )
   MULTIQC( RNASEQ.out, params.multiqc )
 }
+
+output {
+  directory params.outdir
+  mode 'copy'
+  fastqc {
+    index {
+      path 'index.csv'
+    }
+  }
+}

modules/fastqc/main.nf

@@ -1,9 +1,7 @@
-params.outdir = 'results'
 
 process FASTQC {
     tag "FASTQC on $sample_id"
     conda 'bioconda::fastqc=0.12.1'
-    publishDir params.outdir, mode:'copy'
 
     input:
     tuple val(sample_id), path(reads)

modules/multiqc/main.nf

@@ -1,8 +1,6 @@
-params.outdir = 'results'
 
 process MULTIQC {
     conda 'bioconda::multiqc=1.25'
-    publishDir params.outdir, mode:'copy'
 
     input:
     path '*'
@@ -11,6 +9,9 @@ process MULTIQC {
     output:
     path 'multiqc_report.html', emit: report
 
+    publish:
+    report >> 'multiqc'
+
     script:
     """
     cp $config/* .

modules/rnaseq.nf

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