From 2690963d62793bf4259aff92c23ed7bc47c83da5 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sun, 27 Oct 2024 15:04:13 +0100
Subject: [PATCH] Update syntax to 2nd prefix

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 main.nf                 | 25 +++++++++++++++----------
 modules/fastqc/main.nf  |  5 +----
 modules/multiqc/main.nf |  5 +----
 modules/rnaseq.nf       |  4 ++++
 nextflow.config         |  2 +-
 5 files changed, 22 insertions(+), 19 deletions(-)

diff --git a/main.nf b/main.nf
index 6a2de3e..8fec52b 100755
--- a/main.nf
+++ b/main.nf
@@ -17,13 +17,6 @@ params.transcriptome = "$baseDir/data/ggal/ggal_1_48850000_49020000.Ggal71.500bp
 params.outdir = "results"
 params.multiqc = "$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'
@@ -33,7 +26,19 @@ 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 )
+  main:
+  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}
+    """
+
+    read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true ) 
+    RNASEQ( params.transcriptome, read_pairs_ch )
+    MULTIQC( RNASEQ.out, params.multiqc )
+  
+  publish:
+    MULTIQC.out.report >> 'multiqc'
 }
diff --git a/modules/fastqc/main.nf b/modules/fastqc/main.nf
index b277003..0a833b8 100644
--- a/modules/fastqc/main.nf
+++ b/modules/fastqc/main.nf
@@ -8,10 +8,7 @@ process FASTQC {
 
     output:
     path "fastqc_${sample_id}_logs", emit: logs
-
-    publish:
-    logs >> 'fastqc'
-
+    
     script:
     """
     fastqc.sh "$sample_id" "$reads"
diff --git a/modules/multiqc/main.nf b/modules/multiqc/main.nf
index 4c20fba..e039b13 100644
--- a/modules/multiqc/main.nf
+++ b/modules/multiqc/main.nf
@@ -4,14 +4,11 @@ process MULTIQC {
 
     input:
     path '*'
-    path 'config'
+    path config
 
     output:
     path 'multiqc_report.html', emit: report
 
-    publish:
-    report >> 'multiqc'
-
     script:
     """
     cp $config/* .
diff --git a/modules/rnaseq.nf b/modules/rnaseq.nf
index b8f45df..98929e1 100644
--- a/modules/rnaseq.nf
+++ b/modules/rnaseq.nf
@@ -16,4 +16,8 @@ workflow RNASEQ {
 
   emit: 
      QUANT.out | concat(FASTQC.out) | collect
+
+  publish:
+    FASTQC.out.logs >> 'fastqc'
+
 }
diff --git a/nextflow.config b/nextflow.config
index 46f24cf..b82f15e 100755
--- a/nextflow.config
+++ b/nextflow.config
@@ -13,7 +13,7 @@
 manifest {
   description = 'Proof of concept of a RNA-seq pipeline implemented with Nextflow'
   author = 'Paolo Di Tommaso'
-  nextflowVersion = '24.04.4'
+  nextflowVersion = '24.10.0'
 }
 
 /*