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Functional, highly-reproducible bioinformatics pipelines
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Author
2019-05-22
Unested picard-markDuplicates.
l-d-s
2019-05-16
example: pass bionix to call.nix pipeline
Justin Bedo
2019-05-16
slurm: renamed from sbatch
Justin Bedo
2019-05-16
sbatch: allow path specification for salloc
Justin Bedo
2019-05-16
stage: fix multicore tagging to work with derivation overriding
Justin Bedo
2019-05-15
edit example to support passing bionix as argument
Justin Bedo
2019-05-14
strip: remove store paths from outputs to minimise closures
Justin Bedo
2019-05-09
strelka: rewrite to use multiple outputs
Justin Bedo
2019-05-09
test: enable minimap and snap tests
Justin Bedo
2019-05-09
fastp: rename run to check for consistency with fastqc
Justin Bedo
2019-05-02
shard-regex: split into separate file to fix exec issues
Justin Bedo
2019-05-02
shard: missing file
Justin Bedo
2019-05-02
shard: Implement some basic sharding for FQ files
Justin Bedo
2019-05-02
samtools-merge: detect correct sorting
Justin Bedo
2019-05-01
Add fastp.
l-d-s
2019-04-30
Add examples and example README
Justin Bedo
2019-04-30
fix example data urls and hashes
Justin Bedo
2019-04-30
cleanup examples and stray files
Justin Bedo
2019-04-18
sbatch: initial slurm implementation
Justin Bedo
2019-04-17
snap: init
Justin Bedo
2019-04-12
minimap2: typo
Justin Bedo
2019-04-12
minimap2: init
Justin Bedo
2019-04-08
grids: add function to include assemblies with annotated VCF
Justin Bedo
2019-04-08
bowtie: sort the output to ensure determinism
Justin Bedo
2019-04-07
modify outputs to ensure determinism
Justin Bedo
2019-04-07
Update example data and expand tests
Justin Bedo
2019-04-07
update stage names to include bionix- prefix
Justin Bedo
2019-03-28
gridss: less chatty logs
Justin Bedo
2019-03-28
gridss: 2.0.0 → 2.2.2
Justin Bedo
2019-03-22
cnvkit: add scatter plots
Justin Bedo
2019-03-22
cnvkit: copy less files
Justin Bedo
2019-03-15
add multicore passthru flag
Justin Bedo
2019-03-13
mosdepth: fix broken pkg link for mosdepth source
Justin Bedo
2019-03-06
api docs: init GRIDSS
Justin Bedo
2019-03-06
api doc: init fastqc
Justin Bedo
2019-03-06
api docs: init facets
Justin Bedo
2019-03-06
api docs: init CNVkit
Justin Bedo
2019-03-06
api docs: init ascatNGS
Justin Bedo
2019-03-06
api docs: fix bwa type annotations
Justin Bedo
2019-03-06
api docs: init bowtie
Justin Bedo
2019-03-06
draft API docs for BWA and strelka
Justin Bedo
2019-03-04
qsub: fix bug
Justin Bedo
2019-03-01
ascat: init
Justin Bedo
2019-03-01
qsub: fix temporary directory cleanup
Justin Bedo
2019-02-15
ref: missing pkg scope on gawk
Justin Bedo
2019-02-11
snpeff: parameterise heap size and default to 31g
Justin Bedo
2019-02-06
qsub: rename flags to qsubFlags to avoid collision
Justin Bedo
2019-02-06
ref-grch38-snpeff-db: fix pkg scope
Justin Bedo
2019-02-06
qsub: parameterise queue and allow arbitrary flags to be passed
Justin Bedo
2019-01-23
stage: change to stdenvNoCC
Justin Bedo
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