hammerlab biokepi issues

hammerlab / biokepi

Bioinformatics Ketrew Pipelines

Apache License 2.0

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issues

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Upping vaxrank version: 0.6.0 -> 0.7.0

#487 julia326 closed 7 years ago
1
Correct typo in vaxrank dependency

#486 armish closed 7 years ago
0
Add cmdstan

#485 e5c opened 7 years ago
0
update location to b37 human_g1k_v37.fasta.gz file

#484 jburos closed 7 years ago
0
Updating b38 dbsnp URL.

#483 julia326 closed 7 years ago
0
Update b38 ref link

#482 julia326 closed 7 years ago
0
Up python tool and Ensembl versions

#481 julia326 closed 7 years ago
0
Provide `wkhtmltopdf` to vaxrank via conda

#480 armish closed 7 years ago
0
Support running with GRCh38 and/or hg38

#479 julia326 closed 7 years ago
3
Provenance on steroids

#478 smondet closed 7 years ago
1
`bam_left_align`'s `~reference_build` argument?

#477 smondet opened 7 years ago
2
Better estimate each job's resource requirements and encode them into Biokepi as defaults

#476 armish opened 7 years ago
1
Topiary fails to auto-detect reference genome for Varscan VCFs

#475 armish opened 7 years ago
0
Make MuTect v1 great again

#474 armish closed 7 years ago
2
Vaxrank to 0.4.4

#473 ihodes closed 7 years ago
0
Call vaxrank from the `output_folder` instead of the default `root`

#472 armish closed 7 years ago
1
MuTect2 can silently fail and output an empty VCF

#471 ihodes opened 7 years ago
0
Fixing b37 Broad links.

#470 julia326 closed 7 years ago
4
Biokepi dbsnp download fails

#469 julia326 closed 7 years ago
0
Condaify all the tools

#468 armish closed 7 years ago
4
NetMHC temp directory can't be on mounted NFS

#467 julia326 closed 7 years ago
0
Vaxrank nodes should save logs

#466 ihodes closed 7 years ago
2
Use local tmp dir for NetMHC family

#465 armish closed 7 years ago
7
Intermittent OptiType issue

#464 tavinathanson closed 7 years ago
4
Bump topiary 1.2.1 and vaxrank 0.4.3

#463 ihodes closed 7 years ago
0
Add Bfx.validate_bam

#462 tavinathanson opened 7 years ago
2
Move more Input.t constructors into Biokepi

#461 ihodes opened 7 years ago
0
Switch to `solvuu-build`

#460 smondet closed 7 years ago
0
samtools: [finish_merged_header] Output header text too long

#459 ihodes closed 7 years ago
0
Udpate samtools to 1.4

#458 ihodes closed 7 years ago
3
Nodes don't appear to wait on gsutil cp to be done

#457 tavinathanson closed 7 years ago
1
Add bcftools

#456 ihodes closed 7 years ago
0
Add delly2

#455 ihodes closed 7 years ago
2
Add Delly2 to Biokepi

#454 ihodes closed 7 years ago
0
Gatk memory setting

#453 ihodes closed 7 years ago
0
First pass of "save" functionality

#452 ihodes closed 7 years ago
9
Fill in the gaps to cover the most basic needs of a bfx pipeline

#451 armish opened 7 years ago
0
Update build

#450 smondet closed 7 years ago
1
Increasing topiary version: 0.1.2 -> 1.2.0

#449 julia326 closed 7 years ago
0
STAR aligner shouldn't do sorting; does in-memory

#448 ihodes closed 7 years ago
0
Fix hlarp hack

#447 hammer opened 7 years ago
1
Separate bwa configs for mem and aln sub-methods

#446 armish closed 7 years ago
1
Default `bwa mem` penalty parameters in biokepi are

#445 armish closed 7 years ago
1
Save JSON/CSV manifests automatically

#444 tavinathanson opened 7 years ago
1
Update mm10 to 87

#443 ihodes closed 7 years ago
0
Cufflinks segfaults on every run

#442 tavinathanson opened 7 years ago
0
Add support for cleaning a BAM via Picard's CleanSam

#441 armish closed 7 years ago
0
Topiary crash

#440 ihodes closed 7 years ago
3
Upping vaxrank version: 0.4.0 -> 0.4.2 (bug fix)

#439 julia326 closed 7 years ago
0
Fix build with Cmdliner 1.0.0

#438 smondet closed 7 years ago
0