Directly generate compressed fastq files from HiSeq split fastqs.

[htsworkflow.git] / htsworkflow / templates / split_fastq.condor

diff --git a/htsworkflow/templates/split_fastq.condor b/htsworkflow/templates/split_fastq.condor
index 127a9c0122edd4351728d62c4b85d129c617bc26..faca698ba64909e81cf77d35321e06e8968f4131 100644 (file)
--- a/htsworkflow/templates/split_fastq.condor
+++ b/htsworkflow/templates/split_fastq.condor
@@ -6,6 +6,6 @@ log={{ logdir }}/fastq.log
 {% if env %}environment="{{env}}"{% endif %}
 
 {% for arg in args %}
-arguments="{{ arg.pyscript }} -o {{ arg.target }} {% for s in arg.sources %}{{ s }} {% endfor %}"
+arguments="{{ arg.pyscript }} {{ arg.compression }} -o {{ arg.target }} {% for s in arg.sources %}{{ s }} {% endfor %}"
 queue
 {% endfor %}