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hammerlab
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biokepi
Bioinformatics Ketrew Pipelines
Apache License 2.0
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Add "sample_name" field to a new fastqc_result product type
#387
ihodes
opened
7 years ago
0
Updating Dockerfile to allow for vaxrank PDF report generation:
#386
julia326
closed
7 years ago
2
Support TTFI implementation of indel_realigner for n bams
#385
ihodes
opened
7 years ago
0
Add a `fastq_of_inputs` like `fastq_of_input`
#384
ihodes
opened
7 years ago
0
Fix b37 decoy failing due to trailing garbage on gunzip
#383
ihodes
closed
7 years ago
2
fix OptiType installation and init procedure
#382
armish
closed
7 years ago
2
WIP: QC improvements
#381
armish
closed
7 years ago
5
Properly name the outputs of Bedtools intersect
#380
ihodes
closed
7 years ago
0
Support InsertSizeMetrics tool from Picard
#379
ihodes
opened
7 years ago
1
Add PEAR for merging overlapping paired-end reads
#378
iskandr
opened
7 years ago
2
Simplify EDSL extensions
#377
smondet
closed
7 years ago
1
Fix the naming hash comparing function types
#376
ihodes
closed
7 years ago
0
Add expression paths to seq2hla results
#375
ihodes
closed
7 years ago
0
Clean-up work-dir after Seq2HLA failures
#374
smondet
closed
7 years ago
1
Seq2Hla needs a cleanup step to remove its workdir if it fails
#373
ihodes
closed
7 years ago
1
Add `graphviz` package to the `Dockerfile`
#372
smondet
closed
7 years ago
1
Python-tools: bump vaxrank version
#371
armish
closed
7 years ago
0
seq2HLA: ban ncurses library from the conda env
#370
armish
closed
7 years ago
0
Do some documentation fixes
#369
smondet
closed
8 years ago
1
Add support for FusionCatcher
#368
iskandr
opened
8 years ago
4
Support PDF and HTML reports of Vaxrank (and update Vaxrank)
#367
ihodes
closed
7 years ago
0
Update PyEnsembl and Vaxrank
#366
ihodes
closed
8 years ago
0
Reference genomes need a new abstractions
#365
ihodes
opened
8 years ago
3
PyEnsemble releases should in subdirectories so that you can have multiple releases for the same organism
#364
ihodes
opened
8 years ago
0
Vaxrank fails on mouse data
#363
ihodes
closed
7 years ago
1
pVAC-Seq
#362
iskandr
opened
8 years ago
3
Sort mm10 karyotypically
#361
ihodes
closed
7 years ago
1
Shorten names that GATK.indel_realign produces
#360
ihodes
closed
8 years ago
0
Implement vcf product
#359
smondet
closed
8 years ago
0
Vaxrank depends on the input BAM having a BAI
#358
ihodes
closed
8 years ago
3
Add Pageant
#357
ihodes
opened
8 years ago
1
Add dependence on .bai of bam file for Vaxrank
#356
ihodes
closed
8 years ago
0
NetMHC: wrap the netMHC wrappers for better environment control
#355
armish
closed
8 years ago
2
Cut a release
#354
ihodes
opened
8 years ago
0
Better tame the NetMHC tool installations
#353
armish
closed
8 years ago
0
Fix module paths in `EDSL.To_workflow`
#352
smondet
closed
8 years ago
1
add gawk as a dependency (for NetMHC stuff)
#351
armish
closed
8 years ago
3
Control filename lengths
#350
smondet
closed
8 years ago
3
Give fragments default names in the Input deriver
#349
ihodes
closed
8 years ago
1
Add OCaml 4.03.0 to the travis builds
#348
smondet
closed
8 years ago
3
NetMHC: support for installing netmhc 3.4
#347
armish
closed
8 years ago
0
ungzip isn't requesting enough resources?
#346
ihodes
closed
7 years ago
1
Fetch public data from Google Genomics public data sets if we're running on GCP
#345
hammer
closed
7 years ago
1
add support for installing relevant NetMHC tools
#344
armish
closed
8 years ago
2
Need a local cache/repo of tools and references
#343
ihodes
closed
7 years ago
1
Add bedtools intersect for VCF files to TTFI
#342
ihodes
closed
8 years ago
0
Add samblaster tool
#341
arahuja
closed
8 years ago
0
More dockerfile improvements
#340
smondet
closed
8 years ago
0
Fix bedtools bamtofastq
#339
arahuja
closed
8 years ago
6
Some clean-up nodes do not use the `Machine.run_program`
#338
smondet
opened
8 years ago
0
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