From 45d5d3a8c8d9adb03ad148607a27659a2c7e4d27 Mon Sep 17 00:00:00 2001
From: Charles Plessy <charles.plessy@oist.jp>
Date: Wed, 17 Apr 2024 17:29:27 +0900
Subject: [PATCH] Run assemblyscan instead of fastqc

---
 workflows/pairalign.nf | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/workflows/pairalign.nf b/workflows/pairalign.nf
index ee29079..ebf3e17 100644
--- a/workflows/pairalign.nf
+++ b/workflows/pairalign.nf
@@ -5,6 +5,7 @@
 */
 
 include { FASTQC                 } from '../modules/nf-core/fastqc/main'
+include { ASSEMBLYSCAN           } from '../modules/nf-core/assemblyscan/main'
 include { MULTIQC                } from '../modules/nf-core/multiqc/main'
 include { paramsSummaryMap       } from 'plugin/nf-validation'
 include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'
@@ -30,11 +31,11 @@ workflow PAIRALIGN {
     //
     // MODULE: Run FastQC
     //
-    FASTQC (
+    ASSEMBLYSCAN (
         ch_samplesheet
     )
-    ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]})
-    ch_versions = ch_versions.mix(FASTQC.out.versions.first())
+    ch_multiqc_files = ch_multiqc_files.mix(ASSEMBLYSCAN.out.json.collect{it[1]})
+    ch_versions = ch_versions.mix(ASSEMBLYSCAN.out.versions.first())
 
     //
     // Collate and save software versions