From 8b60491004de1fd5688985f0947ec460cc995d5c Mon Sep 17 00:00:00 2001
From: jessicaw9910 <jessbwhite@gmail.com>
Date: Thu, 18 Jul 2024 18:38:53 -0400
Subject: [PATCH] fixed persistent adapter_fasta issue

---
 nextflow/main.nf | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/nextflow/main.nf b/nextflow/main.nf
index 348303b..5ad3563 100644
--- a/nextflow/main.nf
+++ b/nextflow/main.nf
@@ -67,7 +67,7 @@ include { BAM_QC } from './subworkflows/bam_qc.nf' addParams(OUTPUT: "${params.o
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    LOAD FASTQ FILES AS CHANNEL
+    LOAD FILES
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
@@ -75,6 +75,11 @@ Channel
     .fromFilePairs ( params.fastq, checkIfExists: true )
     .set { fastq_ch }
 
+if ( params.adapterFASTA ){
+    adapter_fasta = file(params.adapterFASTA)
+    if( !adapter_fasta.exists() ) exit 1, "Genome chrom sizes file not found: ${params.adapterFASTA}"
+}
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     WORKFLOWS
@@ -90,11 +95,6 @@ workflow FASTQC_FASTQ {
 }
 
 workflow FASTP_FASTQ {
-    if ( params.adapterFASTA ){
-        adapter_fasta = file(params.adapterFASTA)
-        if( !adapter_fasta.exists() ) exit 1, "Genome chrom sizes file not found: ${params.adapterFASTA}"
-    }
-
     RUN_FASTP ( fastq_ch, adapter_fasta )
     RUN_FASTQC_FASTP ( RUN_FASTP.out.reads )
     RUN_MULTIQC_FASTP (