Annotation API

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

@@ -50,10 +50,11 @@ 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 )
+@WorkflowFn(main=true)
+def MAIN() {
+  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 +1,22 @@
 params.outdir = 'results'
 
-process FASTQC {
-    tag "FASTQC on $sample_id"
-    conda 'fastqc=0.12.1'
-    publishDir params.outdir, mode:'copy'
-
-    input:
-    tuple val(sample_id), path(reads)
-
-    output:
-    path "fastqc_${sample_id}_logs" 
-
-    script:
+@ProcessFn(
+    directives={
+        tag { "FASTQC on $sample.id" }
+        conda 'fastqc=0.12.1'
+        publishDir params.outdir, mode:'copy'
+    },
+    inputs={
+        path { sample.reads }
+    },
+    outputs={
+        path '$file0', { "fastqc_${sample.id}_logs" }
+        emit { path('$file0') }
+    },
+    script=true
+)
+def FASTQC(Sample sample) {
     """
-    fastqc.sh "$sample_id" "$reads"
+    fastqc.sh "$sample.id" "$sample.reads"
     """
 }

modules/index/main.nf

@@ -1,15 +1,19 @@
 
-process INDEX {
-    tag "$transcriptome.simpleName"
-    conda 'salmon=1.10.2'
-
-    input:
-    path transcriptome 
-
-    output:
-    path 'index' 
-
-    script:
+@ProcessFn(
+    directives={
+        tag { transcriptome.simpleName }
+        conda 'salmon=1.10.2'
+    },
+    inputs={
+        path { transcriptome }
+    },
+    outputs={
+        path '$file0', 'index'
+        emit { path('$file0') }
+    },
+    script=true
+)
+def INDEX(Path transcriptome) {
     """
     salmon index --threads $task.cpus -t $transcriptome -i index
     """

modules/multiqc/main.nf

@@ -1,17 +1,21 @@
 params.outdir = 'results'
 
-process MULTIQC {
-    conda 'multiqc=1.17'
-    publishDir params.outdir, mode:'copy'
-
-    input:
-    path('*') 
-    path(config) 
-
-    output:
-    path('multiqc_report.html')
-
-    script:
+@ProcessFn(
+    directives={
+        conda 'multiqc=1.17'
+        publishDir params.outdir, mode:'copy'
+    },
+    inputs={
+        path { files }, stageAs: '*'
+        path { config }
+    },
+    outputs={
+        path '$file0', 'multiqc_report.html'
+        emit { path('$file0') }
+    },
+    script=true
+)
+def MULTIQC(List<Path> files, Path config) {
     """
     cp $config/* .
     echo "custom_logo: \$PWD/logo.png" >> multiqc_config.yaml

modules/quant/main.nf

@@ -1,17 +1,21 @@
 
-process QUANT {
-    tag "$pair_id"
-    conda 'salmon=1.10.2'
-
-    input:
-    path index 
-    tuple val(pair_id), path(reads) 
-
-    output:
-    path pair_id 
-
-    script:
+@ProcessFn(
+    directives={
+        tag { pair.id }
+        conda 'salmon=1.10.2'
+    },
+    inputs={
+        path { index }
+        path { pair.reads }
+    },
+    outputs={
+        path '$file0', { pair.id }
+        emit { path('$file0') }
+    },
+    script=true
+)
+def QUANT(Path index, Sample pair) {
     """
-    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
     """
 }

modules/rnaseq.nf

@@ -4,16 +4,11 @@ include { INDEX } from './index'
 include { QUANT } from './quant'
 include { FASTQC } from './fastqc'
 
-workflow RNASEQ {
-  take:
-    transcriptome
-    read_pairs_ch
-
-  main: 
-    INDEX(transcriptome)
-    FASTQC(read_pairs_ch)
-    QUANT(INDEX.out, read_pairs_ch)
-
-  emit: 
-     QUANT.out | concat(FASTQC.out) | collect
+@WorkflowFn
+def RNASEQ(transcriptome, read_pairs_ch) {
+  INDEX(transcriptome)
+  FASTQC(read_pairs_ch)
+  QUANT(INDEX.out, read_pairs_ch)
+    | concat(FASTQC.out)
+    | collect
 }