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Attempt to be robust to not having an alignment in our RunXml file
[htsworkflow.git] / htsworkflow / pipelines /
2013-12-06 Diane TroutAfter implementing proper tests get a working implement... tree | commitdiff
2013-12-05 Diane Troutfix typo tree | commitdiff
2013-12-05 Diane TroutMerge branch 'django1.4' of mus.cacr.caltech.edu:htswor... tree | commitdiff
2013-12-05 Diane TroutMerge branch 'django1.4' of mus.cacr.caltech.edu:htswor... tree | commitdiff
2013-12-05 Diane TroutRecent IPAR xml config blocks include the runfolder... tree | commitdiff
2013-12-02 Diane TroutCatch and report another class of exception tree | commitdiff
2013-10-21 Diane TroutMerge remote-tracking branch 'brisby/django1.4' into... tree | commitdiff
2013-10-21 Diane TroutMerge branch 'django1.4' of mus.cacr.caltech.edu:htswor... tree | commitdiff
2013-10-17 Diane TroutMerge branch 'master' into django1.4 tree | commitdiff
2013-07-22 Diane TroutMove version finding code into the util directory. tree | commitdiff
2013-02-01 Diane TroutMake a sample key list to go along with our lane list tree | commitdiff
2013-01-16 dianeAdd more entries to genome version detection map. tree | commitdiff
2013-01-16 Diane TroutSupport scanning HiSeq runs with multiple analyses. tree | commitdiff
2013-01-16 Diane TroutThrown an exception if we can't parse base calling... tree | commitdiff
2013-01-15 Diane TroutStart making documentation for htsworkflow. tree | commitdiff
2013-01-09 Diane TroutA better resolution to a possible circular dependency. tree | commitdiff
2013-01-08 Diane TroutMerge branch 'django1.4' of mus.cacr.caltech.edu:htswor... tree | commitdiff
2013-01-08 Diane TroutTry to make Aligned result directories optional in... tree | commitdiff
2013-01-08 Diane TroutAdd unaligned stats files to hiseq test case tree | commitdiff
2013-01-08 Diane TroutTweak timestamp format. tree | commitdiff
2012-12-14 Diane TroutGerald's time-stamp format was inconsistent. tree | commitdiff
2012-12-13 Diane TroutUse specific time formatting instead of locale '%c' tree | commitdiff
2012-11-29 Diane TroutRemove prints that were being called in test code. tree | commitdiff
2012-11-28 Diane TroutConvert to unittest2 tree | commitdiff
2012-11-28 Diane TroutConvert to unittest2 tree | commitdiff
2012-11-16 Diane TroutFurther attempts to validate RDF models. tree | commitdiff
2012-09-24 Diane TroutMerge changing lane_number to string and sequence findi... tree | commitdiff
2012-09-19 Diane TroutUse htsworkflow ontology to validate various RDF using... tree | commitdiff
2012-09-18 Diane TroutMerge ssh://jumpgate.caltech.edu/var/htsworkflow/htswor... tree | commitdiff
2012-09-18 Diane TroutMerge branch 'master' of mus.cacr.caltech.edu:htsworkflow tree | commitdiff
2012-09-18 Diane TroutProgress using rdf model to link fastqs with flowcell... tree | commitdiff
2012-08-31 Diane TroutOlder rdf library doesn't like unicode strings as nodes tree | commitdiff
2012-08-31 Diane TroutAllow option to save/restore a sequence class to a... tree | commitdiff
2012-08-06 Diane TroutMerge branch 'master' of mus.cacr.caltech.edu:htsworkflow tree | commitdiff
2012-08-06 Diane TroutMerge branch 'master' of mus.cacr.caltech.edu:htsworkflow tree | commitdiff
2012-08-06 Diane TroutTest proper setting of sequence project variable tree | commitdiff
2012-08-02 Diane TroutTest more of the sequences class. tree | commitdiff
2012-07-25 Diane TroutActually we want to capture the unanalyzed lanes if... tree | commitdiff
2012-07-19 Diane TroutAdapt building qseq or srf archives to use SampleKey... tree | commitdiff
2012-07-19 Diane TroutUpdate save_raw_data to SampleKey api tree | commitdiff
2012-07-19 Diane TroutAdd in a few more genomes to detection code tree | commitdiff
2012-07-16 Diane TroutRemove default sequence-format so the new auto-detector... tree | commitdiff
2012-07-14 Diane TroutAttempt to guess raw sequence type for a run. tree | commitdiff
2012-07-13 Diane TroutFix a refactoring error tree | commitdiff
2012-07-12 Diane TroutLook for RTAConfig.xml file generated by pipeline 1... tree | commitdiff
2012-07-12 Diane TroutUse lane 1s matrix when pipeline was set to build matri... tree | commitdiff
2012-07-12 Diane TroutClean up flowcell ID detection and add support for... tree | commitdiff
2012-07-12 Diane TroutRe-enable some suppressed tests and update them for... tree | commitdiff
2012-07-12 Diane Troutwhitespace fix. tree | commitdiff
2012-07-11 Diane TroutTest reading the xml out of a file too. tree | commitdiff
2012-07-10 Diane TroutFix import statement and typos for genomemap tree | commitdiff
2012-07-10 Diane TroutCreate a class to convert contig names into genome... tree | commitdiff
2012-07-10 Diane TroutGuess genome name for building compressed mapping count... tree | commitdiff
2012-07-07 Diane TroutUse sample keys when looking up lane parameters. tree | commitdiff
2012-07-06 Diane TroutA few python 2.6 test case incompatibilities. tree | commitdiff
2012-07-06 Diane TroutSwitch to regular dictionary instead of ordered dictionary. tree | commitdiff
2012-07-05 Diane TroutMassively rework eland file finding and indexing. tree | commitdiff
2012-07-05 Diane TroutRename chromosome in hiseq test set to match our fake... tree | commitdiff
2012-06-30 Diane TroutDisable debug messages for each scanned eland file... tree | commitdiff
2012-06-30 Diane TroutMerge branch 'master' of mus.cacr.caltech.edu:htsworkflow tree | commitdiff
2012-06-30 Diane TroutSupport multiple having an eland file split into multip... tree | commitdiff
2012-06-30 Diane TroutSome minor tweaks to rta 1.12 testing. tree | commitdiff
2012-06-30 Diane TroutProperly code in tabs for simulated hiseq export files tree | commitdiff
2012-06-30 Diane TroutUse different tags indicating gerald or casava style... tree | commitdiff
2012-06-21 Diane TroutMerge ssh://jumpgate.caltech.edu/var/htsworkflow/htswor... tree | commitdiff
2012-06-12 Diane TroutAdd a software (name) property to firecrest, ipar,... tree | commitdiff
2012-06-11 Diane TroutReturn a gerald version number as a number and not... tree | commitdiff
2012-06-02 Diane TroutSplit lane parameters into seperate classes for GA... tree | commitdiff
2012-05-25 Diane TroutMerge ssh://jumpgate.caltech.edu/var/htsworkflow/htswor... tree | commitdiff
2012-05-25 Diane TroutMerge ssh://jumpgate.caltech.edu/var/htsworkflow/htswor... tree | commitdiff
2012-05-16 Diane TroutMerge branch 'master' of mus.cacr.caltech.edu:htsworkflow tree | commitdiff
2012-05-16 Diane Troutupdate summary.py to extract data from HiSeq runs. tree | commitdiff
2012-05-15 Diane TroutFix bugs introduduced by the improved HiSeq runfolder... tree | commitdiff
2012-05-12 Diane TroutMerge branch 'master' of mus.cacr.caltech.edu:htsworkflow tree | commitdiff
2012-05-10 Diane TroutMinimal changes needed to get raw data archived for... tree | commitdiff
2012-04-13 Diane TroutMerge branch 'master' of mus.cacr.caltech.edu:htsworkflow tree | commitdiff
2012-04-12 Diane TroutExtend the adapter id field to support the dual indexed... tree | commitdiff
2012-03-27 Diane TroutMerge branch 'master' of mus.cacr.caltech.edu:htsworkflow tree | commitdiff
2012-03-26 Diane TroutSwitch to lxml for parsing the summary file. tree | commitdiff
2012-03-23 Diane TroutApparently I forgot to remove a parameter why creating... tree | commitdiff
2012-03-08 Diane TroutActually if I provide an output file, I want to write... tree | commitdiff
2012-03-07 Diane TroutForgot to add split attribute to __eq__ test. tree | commitdiff
2012-03-06 Diane TroutSupport scanning for split fastq files generated by... tree | commitdiff
2012-03-06 Diane TroutAdd module to convert multiple fastq files into a singl... tree | commitdiff
2012-03-05 Diane TroutUse named tuple for sequence flowcell/start/stop/projec... tree | commitdiff
2012-03-02 Diane TroutCore functions for saving and finding fastq files gener... tree | commitdiff
2012-03-01 Diane TroutRemove some debug prints tree | commitdiff
2012-03-01 Diane TroutSimulate a HiSeq runfolder. tree | commitdiff
2011-12-20 Diane TroutMerge branch 'master' of mus.cacr.caltech.edu:htsworkflow tree | commitdiff
2011-12-20 Diane Troutwhitespace reformatting tree | commitdiff
2011-12-20 Diane TroutRemove eXecute bit from modules tree | commitdiff
2011-11-22 Diane TroutAdd a method to override command used to convert srf... tree | commitdiff
2011-11-05 Diane TroutMerge branch 'master' of mus.cacr.caltech.edu:htsworkflow tree | commitdiff
2011-11-04 Diane TroutUse a logger initialized to the module name much more... tree | commitdiff
2011-10-21 Diane TroutYes generate regular gerald config file. tree | commitdiff
2011-10-10 Diane TroutRemove ReadPrep and Thumbnail_Images being generated... tree | commitdiff
2011-10-10 Diane TroutDon't need to duplicate %t tile in srf command tree | commitdiff
2011-10-06 Diane TroutAdd the ability to specify a flowcell id instead of... tree | commitdiff
2011-10-04 Diane TroutAdd support for flowcells analyzed with Casava 1.7 tree | commitdiff
2011-09-19 Diane TroutOutput samples that don't have index sequence as well. tree | commitdiff
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htsworkflow sequencing LIMS software