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48 Open 294 Closed
48 Open 294 Closed
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Issues list

Fix importFile documentation
#480 opened Feb 18, 2017 by cket
@cket
Pass job to germline docker call fuctions in progress
#478 opened Nov 24, 2016 by jpfeil
1
@jpfeil
Fix ADAM/GATK pipeline input errors
#471 opened Oct 12, 2016 by jpfeil
GATK Pipeline Validation Testing
#470 opened Oct 11, 2016 by alex-hancock
@jpfeil
3
Make sure stdout and stderr from tools are not suppressed in worker log
#466 opened Sep 17, 2016 by hannes-ucsc
@hannes-ucsc
Request: Accept cram input to toil-exome enhancement
#444 opened Sep 8, 2016 by Jeltje
Wrap ADAM pipeline calls in logged timers spark/adam
#435 opened Sep 6, 2016 by fnothaft
@fnothaft
change STAR outSAMunmapped argument
#433 opened Sep 6, 2016 by hbeale
S3 tests should be skipped if bucket can't be accessed bug
#429 opened Aug 31, 2016 by fnothaft
Eliminate config options for approximate input file size enhancement
#427 opened Aug 24, 2016 by hannes-ucsc
Support germline joint genotyping and hard filtering
#426 opened Aug 24, 2016 by jpfeil
Refactor germline shared files download
#425 opened Aug 24, 2016 by jpfeil
Factor Docker version strings out
#424 opened Aug 24, 2016 by fnothaft
Add JEXL expressions to germline config
#423 opened Aug 24, 2016 by jpfeil
Rename check_output parameter to return_stdout
#394 opened Jul 29, 2016 by cmarkello
toil-bwa should throw error on wrong input
#393 opened Jul 29, 2016 by Jeltje
Add cloud pilot quality control workflows firecloud ready spark/adam
#380 opened Jul 25, 2016 by fnothaft
@fnothaft
All external process invocations should be logged
#379 opened Jul 25, 2016 by hannes-ucsc
Point at ADAM 0.20.0 RC for adam-pipeline spark/adam
#369 opened Jul 20, 2016 by fnothaft
@fnothaft
Port remaining tests to unittest.TestCase enhancement
#368 opened Jul 19, 2016 by hannes-ucsc
test_upload_and_download_with_encryption gets into a rut bug
#367 opened Jul 19, 2016 by hannes-ucsc 2.1.0
1
Replace PyTest in setup.py with make prepare like in Toil enhancement
#358 opened Jul 15, 2016 by hannes-ucsc
2
Remove duplicated functions in gatk_processing planned
#330 opened Jun 28, 2016 by jvivian 2.0.0
@jpfeil
1
Print errors to STDERR
#319 opened Jun 24, 2016 by Jeltje
2
Remove author tags from scripts
#310 opened Jun 20, 2016 by fnothaft
@fnothaft
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