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 3ea03509b9de3b8073784584b11dff23c18aea92..faca698ba64909e81cf77d35321e06e8968f4131 100644 (file)
--- a/htsworkflow/templates/split_fastq.condor
+++ b/htsworkflow/templates/split_fastq.condor
@@ -1,11 +1,11 @@
 Universe=vanilla
-executable={{ exe }}
+executable={{ python }}
 error={{ logdir }}/fastq.$(process).out
 output={{ logdir }}/fastq.$(process).out
 log={{ logdir }}/fastq.log
-{% if env %}environment={{ env }}{% endif %}
+{% 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 %}