Use typed process inputs and outputs

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

Author: bentsherman

lib/Sample.groovy

@@ -0,0 +1,14 @@
+
+import java.nio.file.Path
+import nextflow.io.ValueObject
+import nextflow.util.KryoHelper
+
+@ValueObject
+class Sample {
+  String id
+  List<Path> reads
+
+  static {
+    KryoHelper.register(Sample)
+  }
+}

main.nf

@@ -51,9 +51,9 @@ include { MULTIQC } from './modules/multiqc'
  * main script flow
  */
 workflow {
-  read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true ) 
-  RNASEQ( params.transcriptome, read_pairs_ch )
-  MULTIQC( RNASEQ.out, params.multiqc )
+  read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true ).map { args -> new Sample(*args) }
+  RNASEQ( file(params.transcriptome), read_pairs_ch )
+  MULTIQC( RNASEQ.out, file(params.multiqc) )
 }
 
 /* 

modules/fastqc/main.nf

@@ -1,18 +1,18 @@
 params.outdir = 'results'
 
 process FASTQC {
-    tag "FASTQC on $sample_id"
+    tag "FASTQC on $sample.id"
     conda 'fastqc=0.12.1'
     publishDir params.outdir, mode:'copy'
 
     input:
-    tuple val(sample_id), path(reads)
+    Sample sample
 
     output:
-    path "fastqc_${sample_id}_logs" 
+    Path logs = path("fastqc_${sample.id}_logs")
 
     script:
     """
-    fastqc.sh "$sample_id" "$reads"
+    fastqc.sh "$sample.id" "$sample.reads"
     """
 }

modules/index/main.nf

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

modules/multiqc/main.nf

@@ -5,11 +5,11 @@ process MULTIQC {
     publishDir params.outdir, mode:'copy'
 
     input:
-    path('*') 
-    path(config) 
+    List<Path> logs
+    Path config
 
     output:
-    path('multiqc_report.html')
+    Path report = path('multiqc_report.html')
 
     script:
     """

modules/quant/main.nf

@@ -1,17 +1,17 @@
 
 process QUANT {
-    tag "$pair_id"
+    tag "$pair.id"
     conda 'salmon=1.10.2'
 
     input:
-    path index 
-    tuple val(pair_id), path(reads) 
+    Path index
+    Sample pair
 
     output:
-    path pair_id 
+    Path result = path(pair.id)
 
     script:
     """
-    salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
+    salmon quant --threads $task.cpus --libType=U -i $index -1 ${pair.reads[0]} -2 ${pair.reads[1]} -o $pair.id
     """
 }