Update process outputs

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

modules/fastqc/main.nf

@@ -10,12 +10,13 @@ params.outdir = 'results'
         path { sample.reads }
     },
     outputs={
-        path { "fastqc_${sample.id}_logs" }
+        path '$file0', { "fastqc_${sample.id}_logs" }
+        emit { path('$file0') }
     },
     script=true
 )
 def FASTQC(Sample sample) {
     """
-    fastqc.sh "$sample.id" "${sample.reads.join(' ')}"
+    fastqc.sh "$sample.id" "$sample.reads"
     """
 }

modules/index/main.nf

@@ -5,10 +5,11 @@
         conda 'salmon=1.10.2'
     },
     inputs={
-        path { transcriptome } 
+        path { transcriptome }
     },
     outputs={
-        path 'index' 
+        path '$file0', 'index'
+        emit { path('$file0') }
     },
     script=true
 )

modules/multiqc/main.nf

@@ -10,7 +10,8 @@ params.outdir = 'results'
         path { config }
     },
     outputs={
-        path('multiqc_report.html')
+        path '$file0', 'multiqc_report.html'
+        emit { path('$file0') }
     },
     script=true
 )

modules/quant/main.nf

@@ -9,7 +9,8 @@
         path { pair.reads }
     },
     outputs={
-        path { pair.id }
+        path '$file0', { pair.id }
+        emit { path('$file0') }
     },
     script=true
 )