From 0f39d28a3c2df79245c258f5929b55d8eba529b5 Mon Sep 17 00:00:00 2001
From: golobor <goloborodko.anton@gmail.com>
Date: Thu, 3 Jan 2019 13:32:54 -0500
Subject: [PATCH] bugfix fastqc task

---
 distiller.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/distiller.nf b/distiller.nf
index 7d3ba56..146fabd 100644
--- a/distiller.nf
+++ b/distiller.nf
@@ -405,8 +405,8 @@ process fastqc{
 
     """
     TASK_TMP_DIR=\$(mktemp -d -p ${task.distillerTmpDir} distiller.tmp.XXXXXXXXXX)
-    ln -s \"\$(readlink -f ${fastq})\" ./temp_fastqc/${library}.${run}.${chunk}.${side}.fastq.gz
-    fastqc --threads ${task.cpus} -o ./ -f fastq ./temp_fastqc/${library}.${run}.${chunk}.${side}.fastq.gz
+    ln -s \"\$(readlink -f ${fastq})\" \$TASK_TMP_DIR/${library}.${run}.${chunk}.${side}.fastq.gz
+    fastqc --threads ${task.cpus} -o ./ -f fastq \$TASK_TMP_DIR/${library}.${run}.${chunk}.${side}.fastq.gz
     rm -r \$TASK_TMP_DIR
     """