Define workflow inputs and outputs

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

main.nf

@@ -25,24 +25,6 @@
  */
 nextflow.enable.dsl = 2
 
-/*
- * Default pipeline parameters. They can be overriden on the command line eg.
- * given `params.foo` specify on the run command line `--foo some_value`.
- */
-
-params.reads = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
-params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
-params.outdir = "results"
-params.multiqc = "$baseDir/multiqc"
-
-log.info """\
- R N A S E Q - N F   P I P E L I N E
- ===================================
- transcriptome: ${params.transcriptome}
- reads        : ${params.reads}
- outdir       : ${params.outdir}
- """
-
 // import modules
 include { RNASEQ } from './modules/rnaseq'
 include { MULTIQC } from './modules/multiqc'
@@ -51,14 +33,37 @@ include { MULTIQC } from './modules/multiqc'
  * main script flow
  */
 workflow {
-  read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true ) 
-  RNASEQ( params.transcriptome, read_pairs_ch )
-  MULTIQC( RNASEQ.out, params.multiqc )
-}
+  /*
+   * Default pipeline parameters. They can be overriden on the command line eg.
+   * given `foo` specify on the run command line `--foo some_value`.
+   */
+  input:
+  Path reads = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
+  Path transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
+  Path multiqc = "$baseDir/multiqc"
+  String outdir = "results"
 
-/* 
- * completion handler
- */
-workflow.onComplete {
-	log.info ( workflow.success ? "\nDone! Open the following report in your browser --> $params.outdir/multiqc_report.html\n" : "Oops .. something went wrong" )
+  main:
+  log.info """\
+    R N A S E Q - N F   P I P E L I N E
+    ===================================
+    transcriptome: ${transcriptome}
+    reads        : ${reads}
+    outdir       : ${outdir}
+    """
+
+  read_pairs_ch = channel.fromFilePairs( reads, checkIfExists: true ) 
+  RNASEQ( transcriptome, read_pairs_ch )
+  MULTIQC( RNASEQ.out, multiqc )
+
+  /* 
+   * completion handler
+   */
+  workflow.onComplete {
+    log.info ( workflow.success ? "\nDone! Open the following report in your browser --> $outdir/multiqc_report.html\n" : "Oops .. something went wrong" )
+  }
+
+  output:
+  List<Path> rnaseq_outputs = RNASEQ.out
+  Path multiqc_report = MULTIQC.out
 }

modules/fastqc/main.nf

@@ -1,9 +1,7 @@
-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)

modules/multiqc/main.nf

@@ -1,8 +1,6 @@
-params.outdir = 'results'
 
 process MULTIQC {
     conda 'multiqc=1.17'
-    publishDir params.outdir, mode:'copy'
 
     input:
     path('*') 

modules/rnaseq.nf

@@ -1,19 +1,18 @@
-params.outdir = 'results'
-
 include { INDEX } from './index'
 include { QUANT } from './quant'
 include { FASTQC } from './fastqc'
 
 workflow RNASEQ {
   take:
-    transcriptome
-    read_pairs_ch
+    Path transcriptome
+    Path read_pairs_ch
 
   main: 
     INDEX(transcriptome)
     FASTQC(read_pairs_ch)
     QUANT(INDEX.out, read_pairs_ch)
+    outputs = QUANT.out | concat(FASTQC.out) | collect
 
   emit: 
-     QUANT.out | concat(FASTQC.out) | collect
+    List<Path> outputs
 }