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85 Open 142 Closed
85 Open 142 Closed
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Issues list

bam_left_align's ~reference_build argument? question
#477 opened Jul 5, 2017 by smondet
2
Better estimate each job's resource requirements and encode them into Biokepi as defaults enhancement
#476 opened Jun 26, 2017 by armish
1
Topiary fails to auto-detect reference genome for Varscan VCFs
#475 opened Jun 23, 2017 by armish
MuTect2 can silently fail and output an empty VCF bug
#471 opened May 25, 2017 by ihodes
Add Bfx.validate_bam target library
#462 opened May 2, 2017 by tavinathanson
2
Move more Input.t constructors into Biokepi enhancement
#461 opened May 2, 2017 by ihodes
Fill in the gaps to cover the most basic needs of a bfx pipeline enhancement target library
#451 opened Apr 19, 2017 by armish
Fix hlarp hack
#447 opened Apr 4, 2017 by hammer
@ihodes
1
Save JSON/CSV manifests automatically enhancement
#444 opened Mar 27, 2017 by tavinathanson
1
Cufflinks segfaults on every run tool-bug
#442 opened Mar 24, 2017 by tavinathanson
Use new hg19 we host bug
#433 opened Feb 27, 2017 by ihodes
1
Implement OptiType pre-filtering step enhancement
#426 opened Feb 14, 2017 by tavinathanson
3
For tools where there is a bioconda recipe is available, use conda for install/ensure procedures enhancement
#417 opened Feb 8, 2017 by armish
@armish
Make generalizable HTML manifest for Bfx.save targets enhancement
#415 opened Feb 6, 2017 by ihodes
Add FastqScreen enhancement
#408 opened Jan 31, 2017 by ihodes
Installing igvxml.0.0.6 fails in test example
#403 opened Jan 4, 2017 by julia326
1
Name library properly in BWA-MEM bug
#401 opened Dec 22, 2016 by ihodes
2
dbsnp for b37 decoy (and probably others) is no longer hostes by the Broad where we expect bug
#398 opened Dec 16, 2016 by ihodes
1
Add "sample_name" field to a new fastqc_result product type enhancement
#387 opened Dec 6, 2016 by ihodes
Support TTFI implementation of indel_realigner for n bams enhancement
#385 opened Dec 1, 2016 by ihodes
Add a fastq_of_inputs like fastq_of_input enhancement
#384 opened Nov 30, 2016 by ihodes
Support InsertSizeMetrics tool from Picard enhancement
#379 opened Oct 27, 2016 by ihodes
1
Add PEAR for merging overlapping paired-end reads enhancement target library
#378 opened Oct 26, 2016 by iskandr
2
Add support for FusionCatcher target library
#368 opened Sep 29, 2016 by iskandr
4
Reference genomes need a new abstractions doc question
#365 opened Sep 27, 2016 by ihodes
3
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