Updated examples

fun-library.nf

@@ -0,0 +1,13 @@
+def getInputForRnaseq( transcriptsPath, readsPath ) {
+
+    def separateTranscriptFromReads = forkCriteria({ tuple -> 
+        trascript: tuple[0]
+        reads: [ tuple[1], tuple[2] ]
+        })
+
+    def reads = Channel.fromFilePairs(readsPath) 
+    Channel.fromPath(transcriptsPath) \
+        | combine( reads ) \
+        | fork(separateTranscriptFromReads) 
+
+}

main1.nf

@@ -100,7 +100,7 @@ process multiqc {
     publishDir params.outdir, mode:'copy'
 
     input:
-    path '*' from quant_ch.mix(fastqc_ch).collect()
+    path 'data*/*' from quant_ch.mix(fastqc_ch).collect()
     path config from params.multiqc
 
     output:

main10.nf

@@ -44,13 +44,13 @@ log.info """\
 include './rnaseq-analysis' params(params)
 
 workflow rnaseqForTranscrip1 {
-    'rnaseq-analysis'( 
+    rnaseq_analysis ( 
         params.transcript1, 
         Channel .fromFilePairs( params.reads, checkExists: true )  )
 }
 
 workflow rnaseqForTranscrip2 {
-    'rnaseq-analysis'( 
+    rnaseq_analysis ( 
         params.transcript2, 
         Channel .fromFilePairs( params.reads, checkExists: true )  )
 }

main11.nf

@@ -43,19 +43,8 @@ log.info """\
 
 include './rnaseq-analysis' params(params)
 
-workflow rnaseqForTranscrip1 {
-    'rnaseq-analysis'( 
-        params.transcript1, 
-        Channel .fromFilePairs( params.reads, checkExists: true )  )
-}
-
-workflow rnaseqForTranscrip2 {
-    'rnaseq-analysis'( 
-        params.transcript2, 
-        Channel .fromFilePairs( params.reads, checkExists: true )  )
-}
 
-workflow manyTranscript {
+workflow {
     reads = Channel .fromFilePairs( 'data/ggal/ggal_*_{1,2}.fq' ) 
     transcripts  = Channel.fromPath('data/ggal/transcriptome_*.fa')
     transcripts
@@ -66,12 +55,7 @@ workflow manyTranscript {
          }
          .set { fork_out }
 
-     'rnaseq-analysis'(fork_out)
-}
-
-workflow {
-    rnaseqForTranscrip1()
-    rnaseqForTranscrip2()
+     rnaseq_analysis(fork_out)
 }
 
 workflow.onComplete {

main12.nf

@@ -43,19 +43,6 @@ log.info """\
 
 include './rnaseq-analysis' params(params)
 
-workflow rnaseqForTranscrip1 {
-    rnaseq_analysis ( 
-        params.transcript1, 
-        Channel .fromFilePairs( params.reads, checkExists: true )  )
-}
-
-workflow rnaseqForTranscrip2 {
-    rnaseq_analysis ( 
-        params.transcript2, 
-        Channel .fromFilePairs( params.reads, checkExists: true )  )
-}
-
-
 
 workflow {
 

main13.nf

@@ -43,18 +43,6 @@ log.info """\
 
 include './rnaseq-analysis' params(params)
 
-workflow rnaseqForTranscrip1 {
-    rnaseq_analysis ( 
-        params.transcript1, 
-        Channel .fromFilePairs( params.reads, checkExists: true )  )
-}
-
-workflow rnaseqForTranscrip2 {
-    rnaseq_analysis ( 
-        params.transcript2, 
-        Channel .fromFilePairs( params.reads, checkExists: true )  )
-}
-
 
 
 workflow {
@@ -63,14 +51,13 @@ workflow {
            trascript: tuple[0]
            reads: [ tuple[1], tuple[2] ]
          })
-         
-    Channel .fromFilePairs( 'data/ggal/ggal_*_{1,2}.fq' ).set {reads} 
+
+    Channel.fromFilePairs( 'data/ggal/ggal_*_{1,2}.fq' ).set {reads} 
     Channel.fromPath('data/ggal/transcriptome_*.fa') \
         | combine( reads ) \
         | fork(separateTranscriptFromReads) \
         | rnaseq_analysis
 
-
 }
 
 workflow.onComplete {

main14.nf

@@ -0,0 +1,66 @@
+/*
+ * Copyright (c) 2013-2019, Centre for Genomic Regulation (CRG).
+ *
+ * This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ *
+ * This Source Code Form is "Incompatible With Secondary Licenses", as
+ * defined by the Mozilla Public License, v. 2.0.
+ *
+ */
+
+
+/*
+ * Proof of concept of a RNAseq pipeline implemented with Nextflow
+ *
+ * Authors:
+ * - Paolo Di Tommaso <[email protected]>
+ * - Emilio Palumbo <[email protected]>
+ * - Evan Floden <[email protected]>
+ */
+nextflow.preview.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 = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
+params.transcripts = "$baseDir/data/ggal/transcriptome_*.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
+ ===================================
+ transcript1  : ${params.transcript1}
+ transcript2  : ${params.transcript2}
+ reads        : ${params.reads}
+ outdir       : ${params.outdir}
+ """
+
+include './rnaseq-analysis' params(params)
+
+
+def getInputForRnaseq( transcriptsPath, readsPath ) {
+
+    def separateTranscriptFromReads = forkCriteria({ tuple -> 
+        trascript: tuple[0]
+        reads: [ tuple[1], tuple[2] ]
+        })
+
+    def reads = Channel.fromFilePairs(readsPath) 
+    Channel.fromPath(transcriptsPath) \
+        | combine( reads ) \
+        | fork(separateTranscriptFromReads) 
+
+}
+
+workflow {
+    getInputForRnaseq(params.transcripts, params.reads) | rnaseq_analysis
+}
+
+workflow.onComplete {
+	log.info ( workflow.success ? "\nDone! Open the following report in your browser --> $params.outdir/multiqc_report.html\n" : "Oops .. something went wrong" )
+}

main15.nf

@@ -0,0 +1,57 @@
+/*
+ * Copyright (c) 2013-2019, Centre for Genomic Regulation (CRG).
+ *
+ * This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ *
+ * This Source Code Form is "Incompatible With Secondary Licenses", as
+ * defined by the Mozilla Public License, v. 2.0.
+ *
+ */
+
+
+/*
+ * Proof of concept of a RNAseq pipeline implemented with Nextflow
+ *
+ * Authors:
+ * - Paolo Di Tommaso <[email protected]>
+ * - Emilio Palumbo <[email protected]>
+ * - Evan Floden <[email protected]>
+ */
+nextflow.preview.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 = "$baseDir/data/ggal/ggal_gut_{1,2}.fq"
+params.transcripts = "$baseDir/data/ggal/transcriptome_*.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
+ ===================================
+ transcript1  : ${params.transcript1}
+ transcript2  : ${params.transcript2}
+ reads        : ${params.reads}
+ outdir       : ${params.outdir}
+ """
+
+include './rnaseq-analysis-2' params(params)
+include './fun-library'
+
+workflow {
+	main:
+	getInputForRnaseq(params.transcripts, params.reads) | rnaseq_analysis
+	publish:
+	rnaseq_analysis.out.fastqc to: 'results/fastqc_files'
+	rnaseq_analysis.out.quant to: 'results/quant_files'
+	rnaseq_analysis.out.multiqc to: 'results/multiqc_report'
+}
+
+workflow.onComplete {
+	log.info ( workflow.success ? "\nDone! Open the following report in your browser --> $params.outdir/multiqc_report.html\n" : "Oops .. something went wrong" )
+}

main2.nf

@@ -100,7 +100,7 @@ process multiqc {
     publishDir params.outdir, mode:'copy'
 
     input:
-    path '*' from quant_ch.mix(fastqc_ch).collect()
+    path 'data*/*' from quant_ch.mix(fastqc_ch).collect()
     path config from params.multiqc
 
     output:

main3.nf

@@ -42,7 +42,7 @@ log.info """\
 
 Channel
     .fromFilePairs( params.reads, checkExists:true )
-    .into { read_pairs_ch; read_pairs2_ch }
+    .set{ read_pairs_ch }
 
 
 process index {
@@ -100,7 +100,7 @@ process multiqc {
     publishDir params.outdir, mode:'copy'
 
     input:
-    path '*' 
+    path 'data*/*' 
     path config 
 
     output:

main4.nf

@@ -42,7 +42,7 @@ log.info """\
 
 Channel
     .fromFilePairs( params.reads, checkExists:true )
-    .into { read_pairs_ch; read_pairs2_ch }
+    .set{ read_pairs_ch }
 
 
 process index {
@@ -100,7 +100,7 @@ process multiqc {
     publishDir params.outdir, mode:'copy'
 
     input:
-    path '*' 
+    path 'data*/*' 
     path config 
 
     output:
@@ -119,7 +119,7 @@ workflow {
 
     quant( index.out, read_pairs_ch )
 
-    fastqc( read_pairs2_ch )
+    fastqc( read_pairs_ch )
 
     multiqc( 
             quant.out.mix(fastqc.out).collect(),  

main8.nf

@@ -43,7 +43,7 @@ include './rnaseq-analysis' params(params)
 
 
 workflow {
-    'rnaseq-analysis'( 
+    rnaseq_analysis ( 
         params.transcriptome, 
         Channel .fromFilePairs( params.reads, checkExists: true )  )
 }

main9.nf

@@ -42,19 +42,19 @@ log.info """\
 include './rnaseq-analysis' params(params)
 
 workflow rnaseqForTranscrip1 {
-    'rnaseq-analysis'( 
+    rnaseq_analysis ( 
         params.transcriptome, 
         Channel .fromFilePairs( params.reads, checkExists: true )  )
 }
 
 workflow rnaseqForTranscrip2 {
-    'rnaseq-analysis'( 
+    rnaseq_analysis ( 
         params.transcriptome, 
         Channel .fromFilePairs( params.reads, checkExists: true )  )
 }
 
 workflow {
-    'rnaseq-analysis'( 
+    rnaseq_analysis ( 
         params.transcriptome, 
         Channel .fromFilePairs( params.reads, checkExists: true )  )
 }

rnaseq-analysis-2.nf

@@ -0,0 +1,30 @@
+nextflow.preview.dsl=2
+
+include index from './rnaseq-processes-2' params(params)
+include quant from './rnaseq-processes-2' params(params)
+include fastqc from './rnaseq-processes-2' params(params)
+include multiqc from './rnaseq-processes-2' params(params)
+
+
+workflow rnaseq_analysis {
+    get: 
+        transcriptome
+        read_pairs_ch
+
+    main:
+        index( transcriptome )
+
+        quant( index.out, read_pairs_ch )
+
+        fastqc( read_pairs_ch )
+
+        multiqc( 
+                quant.out.mix(fastqc.out).collect(),  
+                params.multiqc )
+
+    emit:
+        quant = quant.out
+        fastqc = fastqc.out   
+        multiqc = multiqc.out
+}
+