issues
search
hammerlab
/
biokepi
Bioinformatics Ketrew Pipelines
Apache License 2.0
27
stars
4
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Add cDNA for the mm10 genome
#437
armish
closed
7 years ago
1
Add Picard.reorder_sam
#436
ihodes
closed
7 years ago
1
Fix build of one test + improve travis build
#435
smondet
closed
7 years ago
1
PR #431 didn't build all the tests
#434
smondet
closed
7 years ago
2
Use new hg19 we host
#433
ihodes
opened
7 years ago
1
Bump topiary version and add multiple VCF support
#432
armish
closed
7 years ago
2
Add fastq_of_input case for Input.t.Bam
#431
ihodes
closed
7 years ago
1
Bump pyensembl version to make it compatible with the latest versions of pygenomics tools
#430
armish
closed
7 years ago
1
Add BAM to BAI to the TTFI
#429
tavinathanson
closed
7 years ago
3
Edsl.concat: fix and improve
#428
smondet
closed
7 years ago
1
Produce cmts
#427
ihodes
closed
7 years ago
3
Implement OptiType pre-filtering step
#426
tavinathanson
opened
7 years ago
3
Use our own (ordered) version of b38
#425
ihodes
closed
7 years ago
2
Make biokepi use master branch igvxml
#424
ihodes
closed
7 years ago
12
OptiType does not use razerS3 to filter to HLA reads prior to running
#423
tavinathanson
closed
7 years ago
6
Add dbSNP URL for b38
#422
ihodes
closed
7 years ago
0
GATK.bqsr depends on the faidx of the reference
#421
ihodes
closed
7 years ago
0
Use hammerlab link to a sorted mm10 fa
#420
ihodes
closed
7 years ago
0
OptiType fails sometimes with BAM not found
#419
tavinathanson
closed
7 years ago
26
OptiType fails to run with the current setup
#418
armish
closed
7 years ago
2
For tools where there is a bioconda recipe is available, use conda for install/ensure procedures
#417
armish
opened
7 years ago
0
Make Biokepi easier to get going with with minimal OCaml knowledge/time
#416
ihodes
closed
6 years ago
0
Make generalizable HTML manifest for Bfx.save targets
#415
ihodes
opened
7 years ago
0
Create Ppx_deriving_of_cmdliner (seperate repo) to make pipelines easier to make
#414
ihodes
closed
7 years ago
1
Add a Bfx.save (moving results to a final directory, add to a manifest)
#413
ihodes
closed
6 years ago
1
Kallisto should depend on its FASTQ input
#412
ihodes
closed
7 years ago
0
Export Biokepi.EDSL.Library.Input.bam_sample
#411
ihodes
closed
7 years ago
0
Add kallisto cufflinks to ttfi
#410
ihodes
closed
7 years ago
2
Add a Stdlib transform from Input.t to TTFI Bam
#409
ihodes
closed
7 years ago
1
Add FastqScreen
#408
ihodes
opened
7 years ago
0
Update vaxrank to 0.4.0
#407
ihodes
closed
7 years ago
1
Update Vaxrank to 0.3.1
#406
ihodes
closed
7 years ago
0
Better input management in the EDSL
#405
smondet
closed
7 years ago
0
When linking input files into the work dir, need to make their names unique
#404
ihodes
closed
7 years ago
0
Installing igvxml.0.0.6 fails in test example
#403
julia326
opened
7 years ago
1
Expose Samtools.merge_bams options in EDSL
#402
ihodes
closed
7 years ago
0
Name library properly in BWA-MEM
#401
ihodes
opened
7 years ago
2
Downgrade conda so we can do work
#400
ihodes
closed
7 years ago
0
Don't copy Sambamba for install
#399
ihodes
closed
7 years ago
0
dbsnp for b37 decoy (and probably others) is no longer hostes by the Broad where we expect
#398
ihodes
opened
7 years ago
1
Add region to the indel-realigner target name
#397
ihodes
closed
7 years ago
0
Output BAM instead of SAM from Sambamba
#396
ihodes
closed
7 years ago
0
Fix Sambamba install
#395
ihodes
closed
7 years ago
0
Add Sambamba to default toolkit
#394
ihodes
closed
7 years ago
0
Add Sambamba
#393
ihodes
closed
7 years ago
0
Add sambamba
#392
ihodes
closed
7 years ago
0
Add FreeBayes bamleftalign
#391
ihodes
closed
7 years ago
1
Add FreeBayes
#390
ihodes
closed
7 years ago
0
Fix build with omake 0.10.1
#389
smondet
closed
7 years ago
2
Update Vaxrank to 0.3.0 and its arguments/defaults
#388
ihodes
closed
7 years ago
5
Previous
Next