From ae125745eeca97e26a05ca34730727ba238b31e1 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Wed, 6 Sep 2023 23:33:41 -0400
Subject: [PATCH] fix: don't use labels starting with process_ for output dir
 paths

---
 conf/modules.config | 2 +-
 modules/local/qc.nf | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/conf/modules.config b/conf/modules.config
index 13b9468b..9a8101f1 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -2,7 +2,7 @@
 process {
 
     publishDir = [
-        path: { task.label ? "${params.outdir}/${task.label.join('/')}/${task.process.tokenize(':')[-1].toLowerCase()}" : "${params.outdir}/${task.process.tokenize(':')[-1].toLowerCase()}" },
+        path: { task.label ? "${params.outdir}/${task.label.findAll { !it.startsWith('process_') }.join('/')}/${task.process.tokenize(':')[-1].toLowerCase()}" : "${params.outdir}/${task.process.tokenize(':')[-1].toLowerCase()}" },
         mode: params.publish_dir_mode,
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
diff --git a/modules/local/qc.nf b/modules/local/qc.nf
index 1bc83bac..91c498b1 100644
--- a/modules/local/qc.nf
+++ b/modules/local/qc.nf
@@ -27,6 +27,7 @@ process FASTQC {
 process FASTQ_SCREEN {
     tag { meta.id }
     label 'qc'
+    label 'process_low'
 
     input:
         tuple val(meta), path(fastq), path(conf)