From 9cef76afbe221731f7e187d2c8694bfb4cd8523e Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Fri, 8 Dec 2023 22:15:53 -0600
Subject: [PATCH] Update process outputs

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 modules/fastqc/main.nf  | 5 +++--
 modules/index/main.nf   | 5 +++--
 modules/multiqc/main.nf | 3 ++-
 modules/quant/main.nf   | 3 ++-
 4 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/modules/fastqc/main.nf b/modules/fastqc/main.nf
index fb7befb..bc49aed 100644
--- a/modules/fastqc/main.nf
+++ b/modules/fastqc/main.nf
@@ -10,12 +10,13 @@ params.outdir = 'results'
         path { sample.reads }
     },
     outputs={
-        path { "fastqc_${sample.id}_logs" }
+        path '$file0', { "fastqc_${sample.id}_logs" }
+        emit { path('$file0') }
     },
     script=true
 )
 def FASTQC(Sample sample) {
     """
-    fastqc.sh "$sample.id" "${sample.reads.join(' ')}"
+    fastqc.sh "$sample.id" "$sample.reads"
     """
 }
diff --git a/modules/index/main.nf b/modules/index/main.nf
index 48a0d3c..b6dee3a 100644
--- a/modules/index/main.nf
+++ b/modules/index/main.nf
@@ -5,10 +5,11 @@
         conda 'salmon=1.10.2'
     },
     inputs={
-        path { transcriptome } 
+        path { transcriptome }
     },
     outputs={
-        path 'index' 
+        path '$file0', 'index'
+        emit { path('$file0') }
     },
     script=true
 )
diff --git a/modules/multiqc/main.nf b/modules/multiqc/main.nf
index 7af90c6..44e4144 100644
--- a/modules/multiqc/main.nf
+++ b/modules/multiqc/main.nf
@@ -10,7 +10,8 @@ params.outdir = 'results'
         path { config }
     },
     outputs={
-        path('multiqc_report.html')
+        path '$file0', 'multiqc_report.html'
+        emit { path('$file0') }
     },
     script=true
 )
diff --git a/modules/quant/main.nf b/modules/quant/main.nf
index 1006cd1..97522d7 100644
--- a/modules/quant/main.nf
+++ b/modules/quant/main.nf
@@ -9,7 +9,8 @@
         path { pair.reads }
     },
     outputs={
-        path { pair.id }
+        path '$file0', { pair.id }
+        emit { path('$file0') }
     },
     script=true
 )