From: Diane Trout <diane@caltech.edu>
Date: Thu, 2 Aug 2012 21:51:41 +0000 (-0700)
Subject: Fix a few more formatting issues with the geo template
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=1c6b470225e71d69ab0157e7bb8c32862887f3b7

Fix a few more formatting issues with the geo template
---

diff --git a/htsworkflow/templates/geo_submission.soft b/htsworkflow/templates/geo_submission.soft
index 19e6faa..969ff53 100644
--- a/htsworkflow/templates/geo_submission.soft
+++ b/htsworkflow/templates/geo_submission.soft
@@ -1,7 +1,5 @@
-{% for name, value in series %}{{name}} = {{value}}
-{% endfor %}
-{% for row in samples %}
-^SAMPLE={{row.name}}
+{% for name, value in series %}{{name}}={{value}}
+{% endfor %}{% for row in samples %}^SAMPLE={{row.name}}
 !Sample_type=SRA
 !Sample_title={{row.name}}
 !Sample_series_id={{ series_id }}
@@ -34,7 +32,7 @@
 !Sample_raw_file_read_length_{{forloop.counter}}={{raw.read_length}}
 !Sample_raw_file_instrument_model_{{forloop.counter}}={{raw.sequencer_model}}
 !Sample_raw_file_checksum_{{forloop.counter}}={{raw.md5sum}}
-!sample_raw_file_single_or_paired-end={{raw.flowcell_type}}{% endfor %}{% for sup in row.supplimental %}
+!sample_raw_file_single_or_paired-end_{{forloop.counter}}={{raw.flowcell_type}}{% endfor %}{% for sup in row.supplimental %}
 !Sample_supplementary_file_{{forloop.counter}}={{sup.filename}}
 !Sample_supplementary_file_checksum_{{forloop.counter}}={{sup.md5sum}}
 {% endfor %}{% endfor %}