From 642dbad5d50fa166db3b91f233968499923c5286 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Tue, 29 Oct 2024 10:10:32 +0100
Subject: [PATCH] Update to second preview

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 main.nf                 | 43 +++++++++++++++++++++++++++--------------
 modules/fastqc/main.nf  | 11 ++++-------
 modules/multiqc/main.nf |  3 ---
 modules/quant/main.nf   | 10 +++++-----
 modules/rnaseq.nf       |  9 +++++----
 5 files changed, 43 insertions(+), 33 deletions(-)

diff --git a/main.nf b/main.nf
index ab37c81..8ce4333 100755
--- a/main.nf
+++ b/main.nf
@@ -37,14 +37,6 @@ 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'
 include { MULTIQC } from './modules/multiqc'
@@ -53,17 +45,40 @@ include { MULTIQC } from './modules/multiqc'
  * main script flow
  */
 workflow {
-  read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true ) 
+  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, flat: true )
   RNASEQ( params.transcriptome, read_pairs_ch )
-  MULTIQC( RNASEQ.out, params.multiqc )
+
+  samples_ch = RNASEQ.out.quant
+    | join(RNASEQ.out.fastqc)
+
+  multiqc_ch = RNASEQ.out.quant
+    | concat(RNASEQ.out.fastqc)
+    | map { _id, file -> file }
+    | collect
+  MULTIQC( multiqc_ch, params.multiqc )
+
+  publish:
+  samples_ch >> 'samples'
+  MULTIQC.out >> 'multiqc'
 }
 
 output {
-  directory params.outdir
-  mode 'copy'
-  fastqc {
+  samples {
+    path '.'
     index {
-      path 'index.csv'
+      path 'index.json'
+      mapper { id, quant, fastqc ->
+        [id: id, quant: quant, fastqc: fastqc]
+      }
     }
   }
 }
diff --git a/modules/fastqc/main.nf b/modules/fastqc/main.nf
index d53d396..cb960be 100644
--- a/modules/fastqc/main.nf
+++ b/modules/fastqc/main.nf
@@ -1,19 +1,16 @@
 
 process FASTQC {
-    tag "FASTQC on $sample_id"
+    tag "$sample_id"
     conda 'fastqc=0.12.1'
 
     input:
-    tuple val(sample_id), path(reads)
+    tuple val(sample_id), path(fastq_1), path(fastq_2)
 
     output:
-    path "fastqc_${sample_id}_logs", emit: logs
-
-    publish:
-    logs >> 'fastqc'
+    tuple val(sample_id), path("fastqc_${sample_id}_logs"), emit: logs
 
     script:
     """
-    fastqc.sh "$sample_id" "$reads"
+    fastqc.sh "$sample_id" "$fastq_1 $fastq_2"
     """
 }
diff --git a/modules/multiqc/main.nf b/modules/multiqc/main.nf
index f7c0463..55f811d 100644
--- a/modules/multiqc/main.nf
+++ b/modules/multiqc/main.nf
@@ -9,9 +9,6 @@ process MULTIQC {
     output:
     path('multiqc_report.html'), emit: report
 
-    publish:
-    report >> 'multiqc'
-
     script:
     """
     cp $config/* .
diff --git a/modules/quant/main.nf b/modules/quant/main.nf
index 8459597..027f9d5 100644
--- a/modules/quant/main.nf
+++ b/modules/quant/main.nf
@@ -1,17 +1,17 @@
 
 process QUANT {
-    tag "$pair_id"
+    tag "$sample_id"
     conda 'salmon=1.10.2'
 
     input:
-    path index 
-    tuple val(pair_id), path(reads) 
+    path index
+    tuple val(sample_id), path(fastq_1), path(fastq_2)
 
     output:
-    path pair_id 
+    tuple val(sample_id), path(sample_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 ${fastq_1} -2 ${fastq_2} -o $sample_id
     """
 }
diff --git a/modules/rnaseq.nf b/modules/rnaseq.nf
index b8f45df..6ccad42 100644
--- a/modules/rnaseq.nf
+++ b/modules/rnaseq.nf
@@ -8,12 +8,13 @@ workflow RNASEQ {
   take:
     transcriptome
     read_pairs_ch
- 
-  main: 
+
+  main:
     INDEX(transcriptome)
     FASTQC(read_pairs_ch)
     QUANT(INDEX.out, read_pairs_ch)
 
-  emit: 
-     QUANT.out | concat(FASTQC.out) | collect
+  emit:
+    quant = QUANT.out
+    fastqc = FASTQC.out
 }