From ede362dbf91df9f5118f0122f8bfc09d888cb141 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Fri, 25 Mar 2022 15:28:30 +0100
Subject: [PATCH] Remove duplicate config and sync longread fastqc

---
 conf/modules.config                          | 10 ----------
 subworkflows/local/longread_preprocessing.nf |  2 +-
 2 files changed, 1 insertion(+), 11 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 1052bed..7d50174 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -90,16 +90,6 @@ process {
         ]
     }
 
-    withName: FASTQC_POST {
-        ext.args = '--quiet'
-        ext.prefix = { "${meta.id}_${meta.run_accession}_processed" }
-        publishDir = [
-            path: { "${params.outdir}/fastqc/processed" },
-            mode: 'copy',
-            pattern: '*.html'
-        ]
-    }
-
     withName: CAT_FASTQ {
         publishDir = [
             path: { "${params.outdir}/prepared_sequences" },
diff --git a/subworkflows/local/longread_preprocessing.nf b/subworkflows/local/longread_preprocessing.nf
index 58968e8..7c7c24b 100644
--- a/subworkflows/local/longread_preprocessing.nf
+++ b/subworkflows/local/longread_preprocessing.nf
@@ -24,7 +24,7 @@ workflow LONGREAD_PREPROCESSING {
                                         [ meta_new, reads ]
                                     }
 
-    FASTQC_POST ( PORECHOP.out.reads )
+    FASTQC_PROCESSED ( PORECHOP.out.reads )
     ch_versions = ch_versions.mix(PORECHOP.out.versions.first())
     ch_multiqc_files = ch_multiqc_files.mix( FASTQC_PROCESSED.out.zip.collect{it[1]} )