From 614ced318d14832fe57e59503f34ae730e08fc01 Mon Sep 17 00:00:00 2001
From: xgrand <xavier.grand@ens-lyon.fr>
Date: Fri, 18 Aug 2023 14:24:38 +0200
Subject: [PATCH] minor modif porechop/main.nf --input $(readlink -f ../)
---
src/nf_modules/porechop/main.nf | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/nf_modules/porechop/main.nf b/src/nf_modules/porechop/main.nf
index 979db85..579a9e4 100755
--- a/src/nf_modules/porechop/main.nf
+++ b/src/nf_modules/porechop/main.nf
@@ -19,6 +19,6 @@ process porechop {
"""
mkdir ${barcode}
cd ${barcode}/
-porechop --input ../${fastq} -o ${barcode}_merged_porechoped.fastq.gz --threads ${task.cpus}
+porechop --input \$(readlink -f ../${fastq}) -o ${barcode}_merged_porechoped.fastq.gz --threads ${task.cpus}
"""
}
\ No newline at end of file
--
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