Move publish redirects to workflows

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

main.nf

@@ -56,6 +56,9 @@ workflow {
   read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true ) 
   RNASEQ( params.transcriptome, read_pairs_ch )
   MULTIQC( RNASEQ.out, params.multiqc )
+
+  publish:
+  MULTIQC.out >> '.'
 }
 
 /* 

modules/fastqc/main.nf

@@ -10,7 +10,7 @@ process FASTQC {
     path "fastqc_${sample_id}_logs", emit: logs
 
     publish:
-    logs >> '.'
+    logs >> 'fastqc'
 
     script:
     """

modules/multiqc/main.nf

@@ -10,7 +10,7 @@ process MULTIQC {
     path('multiqc_report.html'), emit: report
 
     publish:
-    report >> '.'
+    report >> 'multiqc'
 
     script:
     """

modules/rnaseq.nf

@@ -16,4 +16,7 @@ workflow RNASEQ {
 
   emit: 
      QUANT.out | concat(FASTQC.out) | collect
+
+  publish:
+    FASTQC.out >> '.'
 }