Update syntax

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

main.nf

@@ -47,15 +47,7 @@ workflow {
   }
 }
 
-publish {
+output {
   directory params.outdir
   mode 'copy'
-
-  'fastqc' {
-    path '.'
-  }
-
-  'multiqc' {
-    path '.'
-  }
 }

modules/fastqc/main.nf

@@ -1,19 +1,20 @@
 
 process FASTQC {
-    tag "FASTQC on $sample.id"
+    tag "FASTQC on $id"
     conda 'fastqc=0.12.1'
 
     input:
-    Tuple2<String,List<Path>> sample
+    id      : String
+    reads   : List<Path>
 
     output:
-    Path logs = path("fastqc_${sample.id}_logs")
+    logs    : Path = path("fastqc_${id}_logs")
 
     publish:
     logs >> 'fastqc'
 
     script:
     """
-    fastqc.sh "$sample.id" "$sample.reads"
+    fastqc.sh "$id" "$reads"
     """
 }

modules/index/main.nf

@@ -4,10 +4,10 @@ process INDEX {
     conda 'salmon=1.10.2'
 
     input:
-    Path transcriptome
+    transcriptome   : Path
 
     output:
-    Path index = path('index')
+    index           : Path = path('index')
 
     script:
     """

modules/multiqc/main.nf

@@ -3,11 +3,11 @@ process MULTIQC {
     conda 'multiqc=1.17'
 
     input:
-    List<Path> inputs
-    Path config 
+    inputs  : List<Path>
+    config  : Path 
 
     output:
-    Path report = path('multiqc_report.html')
+    report  : Path = path('multiqc_report.html')
 
     publish:
     report >> 'multiqc'

modules/quant/main.nf

@@ -1,23 +1,24 @@
 
 process QUANT {
-    tag "$pair.id"
+    tag "$id"
     conda 'salmon=1.10.2'
 
     input:
-    Path index
-    Tuple2<String,List<Path>> pair
+    index   : Path
+    id      : String
+    reads   : List<Path>
 
     output:
-    Path quant = path(pair.id) 
+    quant   : Path = path(id) 
 
     script:
     """
     salmon quant \
         --threads $task.cpus \
         --libType=U \
         -i $index \
-        -1 ${pair.reads[0]} \
-        -2 ${pair.reads[1]} \
-        -o $pair.id
+        -1 ${reads[0]} \
+        -2 ${reads[1]} \
+        -o $id
     """
 }

modules/rnaseq.nf

@@ -1,31 +1,31 @@
-params.outdir = 'results'
-
 include { INDEX } from './index'
 include { QUANT } from './quant'
 include { FASTQC } from './fastqc'
 
 workflow RNASEQ {
   take:
-    reads         // Channel<Tuple2<String,List<Path>>>
-    transcriptome // Path
+  reads         : Channel<Tuple2<String,List<Path>>>
+  transcriptome : Path
 
   main: 
-    transcriptome             // Path
-      |> INDEX                // Path 
-      |> set { index }        // Path
+  transcriptome             // Path
+    |> INDEX                // Path 
+    |> set { index }        // Path
 
-    reads                     // Channel<Tuple2<String,List<Path>>>
-      |> map { pair ->
-        QUANT(index, pair)
-      }                       // Channel<Path>
-      |> set { quant }        // Channel<Path>
+  reads                     // Channel<Tuple2<String,List<Path>>>
+    |> map { id, reads ->
+      QUANT(index, id, reads)
+    }                       // Channel<Path>
+    |> set { quant }        // Channel<Path>
 
-    reads                     // Channel<Tuple2<String,List<Path>>>
-      |> map(FASTQC)          // Channel<Path>
-      |> set { fastqc_logs }  // Channel<Path>
+  reads                     // Channel<Tuple2<String,List<Path>>>
+    |> map { id, reads ->
+      FASTQC( id, reads )
+    }                       // Channel<Path>
+    |> set { fastqc_logs }  // Channel<Path>
 
   emit:
-    index
-    quant
-    fastqc_logs
+  index
+  quant
+  fastqc_logs
 }