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 """