From 772d1790d89d2c30073345445420ead6ed4b0ca9 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Tue, 7 May 2024 21:56:51 -0500
Subject: [PATCH] Move publish redirects to workflows

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 main.nf                 | 3 +++
 modules/fastqc/main.nf  | 2 +-
 modules/multiqc/main.nf | 2 +-
 modules/rnaseq.nf       | 3 +++
 4 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/main.nf b/main.nf
index fda13ea..3fa1353 100755
--- a/main.nf
+++ b/main.nf
@@ -56,6 +56,9 @@ workflow {
   read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true ) 
   RNASEQ( params.transcriptome, read_pairs_ch )
   MULTIQC( RNASEQ.out, params.multiqc )
+
+  publish:
+  MULTIQC.out >> '.'
 }
 
 /* 
diff --git a/modules/fastqc/main.nf b/modules/fastqc/main.nf
index a0a139c..d53d396 100644
--- a/modules/fastqc/main.nf
+++ b/modules/fastqc/main.nf
@@ -10,7 +10,7 @@ process FASTQC {
     path "fastqc_${sample_id}_logs", emit: logs
 
     publish:
-    logs >> '.'
+    logs >> 'fastqc'
 
     script:
     """
diff --git a/modules/multiqc/main.nf b/modules/multiqc/main.nf
index e2a35a7..f7c0463 100644
--- a/modules/multiqc/main.nf
+++ b/modules/multiqc/main.nf
@@ -10,7 +10,7 @@ process MULTIQC {
     path('multiqc_report.html'), emit: report
 
     publish:
-    report >> '.'
+    report >> 'multiqc'
 
     script:
     """
diff --git a/modules/rnaseq.nf b/modules/rnaseq.nf
index 2f607c1..1146f7a 100644
--- a/modules/rnaseq.nf
+++ b/modules/rnaseq.nf
@@ -16,4 +16,7 @@ workflow RNASEQ {
 
   emit: 
      QUANT.out | concat(FASTQC.out) | collect
+
+  publish:
+    FASTQC.out >> '.'
 }
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