dnanexus-archive viral-ngs issues

dnanexus-archive / viral-ngs

viral-ngs

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update metrics script

#73 tomkinsc closed 5 years ago
2
update dependencies

#72 tomkinsc closed 6 years ago
0
improve / fix figures of merit in analysis applet

#71 dpark01 closed 6 years ago
1
only plot coverage if input bam has reads

#70 tomkinsc closed 6 years ago
1
metrics script fixes, conda env file for script

#69 tomkinsc closed 6 years ago
0
add metrics script

#68 tomkinsc closed 6 years ago
0
add metrics script

#67 tomkinsc closed 6 years ago
0
extend instance autoscaling to support HiSeq4000-size runs

#66 tomkinsc closed 6 years ago
2
Fix assembly analysis applet failures for less than 1x coverage genomes.

#65 dpark01 closed 7 years ago
4
expose viral-ngs-assembly-analysis in releases

#64 dpark01 opened 7 years ago
0
viral-ngs-bwa-count-hits input types

#63 dpark01 closed 7 years ago
1
s/novoalign_options/aligner_options/g

#62 tomkinsc closed 7 years ago
2
Update docker image to v1.13.3

#61 tomkinsc closed 7 years ago
0
Aligner options not being passed to viral-ngs-assembly-analysis

#60 tomkinsc closed 7 years ago
0
Additional reporting

#59 tomkinsc opened 7 years ago
1
Expose --JVMmemory for assemble_trinity, or auto-scale based on instance size

#58 tomkinsc opened 7 years ago
1
scale back deplete instance size

#57 dpark01 closed 7 years ago
1
auto-select demux instance type based on cumulative run size

#56 mlin closed 6 years ago
1
use viral-ngs docker image instead of native install

#55 mlin closed 7 years ago
0
upgrade all applets to 14.04 runtime environment

#54 mlin closed 7 years ago
0
Enable bwa metagenomics by default

#53 yesimon opened 7 years ago
3
Set 24h timeouts

#52 mlin closed 7 years ago
0
investigate metagenomics parallelism

#51 mlin closed 7 years ago
2
script for pushbutton update of featured project

#50 mlin opened 7 years ago
0
demux jobs for hiseq lanes should get bigger instances

#49 dpark01 closed 7 years ago
5
expose --major_cutoff in refine_assembly

#48 dpark01 closed 7 years ago
2
demux failures silently swallowed by dnanexus

#47 dpark01 closed 7 years ago
3
pass --threads param to refine_assembly invocations

#46 dpark01 closed 7 years ago
2
skip depletion assembly

#45 dpark01 opened 7 years ago
0
move gatk & novoalign inputs from scaffold stage to refine stage

#44 dpark01 opened 7 years ago
2
reduce scaffolding params default values

#43 dpark01 closed 7 years ago
2
demux plus: keep multi-lane outputs organized by lane

#42 mlin closed 7 years ago
0
depletion: add hybsel_probe_adapters BLAST database to defaults (#40)

#41 mlin closed 7 years ago
0
Add additional blast depletion database

#40 tomkinsc closed 7 years ago
0
V1.10.1 updates

#39 yifei-men closed 7 years ago
0
index mapped bam files

#38 tomkinsc closed 7 years ago
3
assembly process names output files funny

#37 dpark01 closed 7 years ago
1
fasta fetcher should use the email address from the active user's DNAnexus account

#36 tomkinsc opened 7 years ago
1
Add coverage plot creation to assembly analysis

#35 tomkinsc closed 7 years ago
4
Dynamic assignment of java version

#34 yifei-men closed 7 years ago
3
update to java 8

#33 yifei-men closed 7 years ago
1
Update resources to v1.7.1

#32 yifei-men closed 7 years ago
0
Quote demux opts

#31 yifei-men closed 7 years ago
0
Viral-ngs demux-plus workflow improvement

#30 yifei-men closed 7 years ago
0
update kraken database

#29 dpark01 closed 7 years ago
3
metagenomics applet: upload as it runs?

#28 dpark01 closed 7 years ago
2
Include barcode frequency report among those generated during demux

#27 tomkinsc closed 7 years ago
4
Change Novoalign source to use conda package and separate novoalign.lic file

#26 tomkinsc closed 7 years ago
7
Create reports as part of automatic post-upload workflow

#25 dpark01 closed 7 years ago
9
viral-ngs-human-depletion-multiplex: name the subjobs

#24 mlin closed 8 years ago
1