Progress using rdf model to link fastqs with flowcell/lib metadata.
authorDiane Trout <diane@caltech.edu>
Tue, 18 Sep 2012 18:20:26 +0000 (11:20 -0700)
committerDiane Trout <diane@caltech.edu>
Tue, 18 Sep 2012 18:20:26 +0000 (11:20 -0700)
commit8096174ac7a288f0f2198c90286d5ddab8c59731
tree42c0ee90a59da1ef4a1ac6811679ea72f149e14e
parent5d3908c830a1cded1b3bfde11c8293c05e997ac1
Progress using rdf model to link fastqs with flowcell/lib metadata.

I changed how I was using rdf:type -- the most raw data is now
a 'sequencer_result' and now there's a seperate file_type
attribute to indicate what kind of result file it is.

I renamed find_missing_targets to update_fastq_targets as
in addition to finding what fastqs we need to generate it'll
also download missing flowcell information.

I'm still having trouble fishing out the fastq files so this isn't
ready yet.

Finally minor tweaks to the soft file formatting to try
and get it to render everything without spurious spaces.
htsworkflow/pipelines/sequences.py
htsworkflow/pipelines/test/test_sequences.py
htsworkflow/submission/condorfastq.py
htsworkflow/submission/daf.py
htsworkflow/submission/test/test_condorfastq.py
htsworkflow/templates/geo_fastqs.sparql
htsworkflow/templates/geo_submission.soft