62 Branches 18 Tags

Name		Name	Last commit message	Last commit date
Latest commit esnaultc use specified column to collapse techn repl, in correct helpers.R Aug 20, 2020 efdda24 · Aug 20, 2020 History 1,606 Commits
.buildkite		.buildkite	run both rnaseq and references	Apr 2, 2017
.circleci		.circleci	updates to the docs building during tests	Jun 16, 2020
ci		ci	ensure_docs.py now makes sure links exist in rmd	Jul 15, 2020
config		config	rename config	Mar 8, 2018
docs		docs	add comments to docs	Jul 16, 2020
include		include	update included reference configs to reflect new reference config system	Apr 30, 2020
lib		lib	use specified column to collapse techn repl, in correct helpers.R	Aug 20, 2020
test/test_configs		test/test_configs	fix test config	May 8, 2020
workflows		workflows	add unique samplename preflight check	Aug 19, 2020
wrappers		wrappers	fix wrapper from last commit	May 2, 2020
.gitignore		.gitignore	Separate conda environments;	Apr 30, 2020
.travis.yml		.travis.yml	add colocalization workflow, config, and tests	Nov 28, 2017
README.md		README.md	whitespace to trigger ci	Feb 25, 2020
deploy.py		deploy.py	require destination for deploy script	Dec 14, 2019
requirements-non-r.txt		requirements-non-r.txt	pin snakemake more carefully to avoid cryptic issues that we'll need …	Jun 14, 2020
requirements-r.txt		requirements-r.txt	add lcdbwf R package (and update reqs to include devtools)	Jul 15, 2020

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`lcdb-wf`

A collection of snakemake workflows and tools for common high-throughput sequencing analysis, along with associated infrastructure.

See docs at https://lcdb.github.io/lcdb-wf.

References workflow

DAG for references workflow:

RNA-seq workflow

DAG for RNA-seq workflow:

ChIP-seq workflow

DAG for ChIP-seq workflow: