@@ -12,10 +12,10 @@ task fusioncatcher{ | |||
set -o pipefail | |||
set -e | |||
mkdir -p ${sample_id}/input | |||
mkdir -p ${sample_id}/output | |||
cp ${fastq1} ${sample_id}/input | |||
cp ${fastq2} ${sample_id}/input | |||
mkdir -p ${sample_id}/input/ | |||
mkdir -p ${sample_id}/output/ | |||
cp ${fastq1} ${sample_id}/input/ | |||
cp ${fastq2} ${sample_id}/input/ | |||
/software/fusioncatcher/bin/fusioncatcher \ | |||
-d ${database_dir} \ |