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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 %}
{% 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 %}
queue
{% endfor %}