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Functional, highly-reproducible bioinformatics pipelines
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Author
2018-11-27
Expand README and add simple example pipeline
Justin Bedo
2018-11-26
qsub: output non-retryable errors
Justin Bedo
2018-11-26
qsub: let sleep timing be configurable
Justin Bedo
2018-11-26
qsub: retry qsub if requested
Justin Bedo
2018-11-26
Merge branch 'master' of https://github.com/PapenfussLab/bionix
l-d-s
2018-11-26
Also need config for 'assemble' step.
l-d-s
2018-11-23
qsub: update to check job_state field
Justin Bedo
2018-11-23
qsub: be more specific with qstat polling
Justin Bedo
2018-11-22
Merge branch 'master' of https://github.com/PapenfussLab/bionix
l-d-s
2018-11-22
gridss: restructure gridss pipeline
Justin Bedo
2018-11-22
samtools-sort: handle missing 'none' sorting case
Justin Bedo
2018-11-22
gridss: fix configure file optional string error
Justin Bedo
2018-11-20
Add some typed fetchurl functions
Justin Bedo
2018-11-15
Fix up gridss config file.
l-d-s
2018-11-15
test-tnpair: avoid gridss.call while it's broken
l-d-s
2018-11-15
gridss.softClipsToSplitReads: sort -> sorting
l-d-s
2018-11-15
Syntax.
l-d-s
2018-11-15
Ignore temporary files.
l-d-s
2018-11-15
Need to test config != null
l-d-s
2018-11-15
Merge branch 'master' of https://github.com/PapenfussLab/bionix
l-d-s
2018-11-15
Ignore .DS_Store
l-d-s
2018-11-15
gridss.softClipsToSplitReads: sort ordering is not preserved
Justin Bedo
NB: this breaks gridss.preprocessBam
2018-11-14
Add ensembl mouse transcriptome
Justin Bedo
2018-11-13
Merge branch 'master' of https://github.com/PapenfussLab/bionix
l-d-s
2018-11-12
Attempt to integrate config file into GRIDSS stage
l-d-s
2018-11-12
Function to great ini-style gridss config file.
l-d-s
2018-11-07
Fix to gridss.
l-d-s
2018-11-07
Add bwa to softClipsToSplitReads
l-d-s
2018-11-02
Allow bwa-mem to take gzipped fastq inputs
Justin Bedo
2018-11-02
kallisto: init
Justin Bedo
2018-11-01
samtools-sort: don't sort if already sorted
Justin Bedo
2018-10-29
Split gridss into constituents
Justin Bedo
Wrap each individual command for GRIDSS so that bionix executed the pipeline rather than GRIDSS. This patch introduces a "call" function that executed the whole pipeline in bionix on an arbitrary BAM file. Resolves #10.
2018-10-29
bwa-mem: BWA output is query name sorted
Justin Bedo
2018-10-29
init: samtools-markdup
Justin Bedo
2018-10-29
init: samtools-fixmate
Justin Bedo
2018-10-26
init: mutect
Justin Bedo
2018-10-26
init: samtools-dict
Justin Bedo
2018-10-26
init: cosmic & dbsnp for grch38
Justin Bedo
2018-10-25
Improve type safety of samtools-merge
Justin Bedo
2018-10-25
Simplify types for sorting
Justin Bedo
2018-10-24
Merge branch 'master' of https://github.com/PapenfussLab/bionix
l-d-s
2018-10-24
Add merge to samtools.
l-d-s
2018-10-24
Simplify test expression
Justin Bedo
2018-10-24
Fix platypus bug
Justin Bedo
2018-10-23
Allow building bwa-mem with one core
Justin Bedo
2018-10-23
Simplify infercnv-app
Justin Bedo
2018-10-23
Wrap inferCNV
Justin Bedo
Resolves #8
2018-10-22
name qsub with name of derivation: fixes #7
Justin Bedo
2018-10-17
rename sigterm patch
Justin Bedo
2018-10-09
Simplify default to error in types
Justin Bedo
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