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use autoopen to access fastq files
[htsworkflow.git]
/
htsworkflow
/
pipelines
/
2014-06-10
Diane Trout
use autoopen to access fastq files
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commitdiff
2014-06-10
Diane Trout
Start implementing tool to compute library fastq quality
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commitdiff
2014-06-10
Diane Trout
Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow
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commitdiff
2014-02-18
Diane Trout
Add option to compress fastq file
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commitdiff
2014-01-22
Diane Trout
Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow
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commitdiff
2014-01-08
Diane Trout
Rename stripNamespace strip_namespace
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commitdiff
2013-12-23
Diane Trout
Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow
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commitdiff
2013-12-17
Diane Trout
remove some test code debugging print statements
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commitdiff
2013-12-17
Diane Trout
Merge branch 'django1.4'
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commitdiff
2013-12-10
Diane Trout
Merge branch 'django1.4' of mus.cacr.caltech.edu:htswor...
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commitdiff
2013-12-06
Diane Trout
After implementing proper tests get a working implement...
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commitdiff
2013-12-06
Diane Trout
After implementing proper tests get a working implement...
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commitdiff
2013-12-05
Diane Trout
fix typo
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commitdiff
2013-12-05
Diane Trout
fix typo
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commitdiff
2013-12-05
Diane Trout
Merge branch 'django1.4' of mus.cacr.caltech.edu:htswor...
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commitdiff
2013-12-05
Diane Trout
Merge branch 'django1.4' of mus.cacr.caltech.edu:htswor...
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commitdiff
2013-12-05
Diane Trout
Recent IPAR xml config blocks include the runfolder...
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commitdiff
2013-12-05
Diane Trout
Recent IPAR xml config blocks include the runfolder...
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commitdiff
2013-12-02
Diane Trout
Catch and report another class of exception
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commitdiff
2013-10-21
Diane Trout
Merge remote-tracking branch 'brisby/django1.4' into...
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commitdiff
2013-10-21
Diane Trout
Merge branch 'django1.4' of mus.cacr.caltech.edu:htswor...
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commitdiff
2013-10-17
Diane Trout
Merge branch 'master' into django1.4
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commitdiff
2013-10-17
Diane Trout
Add command line feature to srf command
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commitdiff
2013-10-17
Diane Trout
Dynamically respond to the number of lanes.
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commitdiff
2013-07-22
Diane Trout
Move version finding code into the util directory.
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commitdiff
2013-02-01
Diane Trout
Make a sample key list to go along with our lane list
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commitdiff
2013-01-16
diane
Add more entries to genome version detection map.
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commitdiff
2013-01-16
Diane Trout
Support scanning HiSeq runs with multiple analyses.
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commitdiff
2013-01-16
Diane Trout
Thrown an exception if we can't parse base calling...
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commitdiff
2013-01-15
Diane Trout
Start making documentation for htsworkflow.
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commitdiff
2013-01-09
Diane Trout
A better resolution to a possible circular dependency.
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commitdiff
2013-01-08
Diane Trout
Merge branch 'django1.4' of mus.cacr.caltech.edu:htswor...
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commitdiff
2013-01-08
Diane Trout
Try to make Aligned result directories optional in...
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commitdiff
2013-01-08
Diane Trout
Add unaligned stats files to hiseq test case
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commitdiff
2013-01-08
Diane Trout
Tweak timestamp format.
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commitdiff
2012-12-14
Diane Trout
Gerald's time-stamp format was inconsistent.
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commitdiff
2012-12-13
Diane Trout
Use specific time formatting instead of locale '%c'
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commitdiff
2012-11-29
Diane Trout
Remove prints that were being called in test code.
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commitdiff
2012-11-28
Diane Trout
Convert to unittest2
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commitdiff
2012-11-28
Diane Trout
Convert to unittest2
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commitdiff
2012-11-16
Diane Trout
Further attempts to validate RDF models.
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commitdiff
2012-09-24
Diane Trout
Merge changing lane_number to string and sequence findi...
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commitdiff
2012-09-19
Diane Trout
Use htsworkflow ontology to validate various RDF using...
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commitdiff
2012-09-18
Diane Trout
Merge ssh://jumpgate.caltech.edu/var/htsworkflow/htswor...
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commitdiff
2012-09-18
Diane Trout
Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow
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commitdiff
2012-09-18
Diane Trout
Progress using rdf model to link fastqs with flowcell...
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commitdiff
2012-08-31
Diane Trout
Older rdf library doesn't like unicode strings as nodes
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commitdiff
2012-08-31
Diane Trout
Allow option to save/restore a sequence class to a...
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commitdiff
2012-08-06
Diane Trout
Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow
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commitdiff
2012-08-06
Diane Trout
Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow
tree
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commitdiff
2012-08-06
Diane Trout
Test proper setting of sequence project variable
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commitdiff
2012-08-02
Diane Trout
Test more of the sequences class.
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commitdiff
2012-07-25
Diane Trout
Actually we want to capture the unanalyzed lanes if...
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commitdiff
2012-07-19
Diane Trout
Adapt building qseq or srf archives to use SampleKey...
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commitdiff
2012-07-19
Diane Trout
Update save_raw_data to SampleKey api
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commitdiff
2012-07-19
Diane Trout
Add in a few more genomes to detection code
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commitdiff
2012-07-16
Diane Trout
Remove default sequence-format so the new auto-detector...
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commitdiff
2012-07-14
Diane Trout
Attempt to guess raw sequence type for a run.
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commitdiff
2012-07-13
Diane Trout
Fix a refactoring error
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commitdiff
2012-07-12
Diane Trout
Look for RTAConfig.xml file generated by pipeline 1...
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commitdiff
2012-07-12
Diane Trout
Use lane 1s matrix when pipeline was set to build matri...
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commitdiff
2012-07-12
Diane Trout
Clean up flowcell ID detection and add support for...
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commitdiff
2012-07-12
Diane Trout
Re-enable some suppressed tests and update them for...
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commitdiff
2012-07-12
Diane Trout
whitespace fix.
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commitdiff
2012-07-11
Diane Trout
Test reading the xml out of a file too.
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commitdiff
2012-07-10
Diane Trout
Fix import statement and typos for genomemap
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commitdiff
2012-07-10
Diane Trout
Create a class to convert contig names into genome...
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commitdiff
2012-07-10
Diane Trout
Guess genome name for building compressed mapping count...
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commitdiff
2012-07-07
Diane Trout
Use sample keys when looking up lane parameters.
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commitdiff
2012-07-06
Diane Trout
A few python 2.6 test case incompatibilities.
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commitdiff
2012-07-06
Diane Trout
Switch to regular dictionary instead of ordered dictionary.
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commitdiff
2012-07-05
Diane Trout
Massively rework eland file finding and indexing.
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commitdiff
2012-07-05
Diane Trout
Rename chromosome in hiseq test set to match our fake...
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commitdiff
2012-06-30
Diane Trout
Disable debug messages for each scanned eland file...
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commitdiff
2012-06-30
Diane Trout
Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow
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commitdiff
2012-06-30
Diane Trout
Support multiple having an eland file split into multip...
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commitdiff
2012-06-30
Diane Trout
Some minor tweaks to rta 1.12 testing.
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commitdiff
2012-06-30
Diane Trout
Properly code in tabs for simulated hiseq export files
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commitdiff
2012-06-30
Diane Trout
Use different tags indicating gerald or casava style...
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commitdiff
2012-06-21
Diane Trout
Merge ssh://jumpgate.caltech.edu/var/htsworkflow/htswor...
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commitdiff
2012-06-12
Diane Trout
Add a software (name) property to firecrest, ipar,...
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commitdiff
2012-06-11
Diane Trout
Return a gerald version number as a number and not...
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commitdiff
2012-06-02
Diane Trout
Split lane parameters into seperate classes for GA...
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commitdiff
2012-05-25
Diane Trout
Merge ssh://jumpgate.caltech.edu/var/htsworkflow/htswor...
tree
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commitdiff
2012-05-25
Diane Trout
Merge ssh://jumpgate.caltech.edu/var/htsworkflow/htswor...
tree
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commitdiff
2012-05-16
Diane Trout
Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow
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commitdiff
2012-05-16
Diane Trout
update summary.py to extract data from HiSeq runs.
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commitdiff
2012-05-15
Diane Trout
Fix bugs introduduced by the improved HiSeq runfolder...
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commitdiff
2012-05-12
Diane Trout
Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow
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commitdiff
2012-05-10
Diane Trout
Minimal changes needed to get raw data archived for...
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commitdiff
2012-04-13
Diane Trout
Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow
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commitdiff
2012-04-12
Diane Trout
Extend the adapter id field to support the dual indexed...
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commitdiff
2012-03-27
Diane Trout
Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow
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commitdiff
2012-03-26
Diane Trout
Switch to lxml for parsing the summary file.
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commitdiff
2012-03-23
Diane Trout
Apparently I forgot to remove a parameter why creating...
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commitdiff
2012-03-08
Diane Trout
Actually if I provide an output file, I want to write...
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commitdiff
2012-03-07
Diane Trout
Forgot to add split attribute to __eq__ test.
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commitdiff
2012-03-06
Diane Trout
Support scanning for split fastq files generated by...
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commitdiff
2012-03-06
Diane Trout
Add module to convert multiple fastq files into a singl...
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commitdiff
2012-03-05
Diane Trout
Use named tuple for sequence flowcell/start/stop/projec...
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