Adding quinine QC functions, and quinine_pipelines (resolves #380)#381
Open
fnothaft wants to merge 16 commits intoBD2KGenomics:masterfrom
Open
Adding quinine QC functions, and quinine_pipelines (resolves #380)#381fnothaft wants to merge 16 commits intoBD2KGenomics:masterfrom
fnothaft wants to merge 16 commits intoBD2KGenomics:masterfrom
Conversation
…enomics#210) Adds a local mode to the ADAM pipeline where Spark runs in local mode with the maximum number of cores on the machine. This requires a local-dir switch too, for pointing ADAM to the data directory.
Adds native-adam-path option to adam-pipeline.
| required=True) | ||
| __add_common_args(parser_hs) | ||
|
|
||
| # add arguments for contaimination estimation |
fnothaft
force-pushed
the
issues/380-quinine
branch
7 times, most recently
from
6881e4a to
eed1ef8
Compare
…mics#380) * Adds the quinine tool (https://github.com/bigdatagenomics/quinine) along with helper functions for running QC on targeted sequencing panels, RNA-seq data, and for estimating sample contamination. * Instantiates these as command line tools in `toil_scripts.quinine_pipelines.metrics`.
fnothaft
added a commit
to fnothaft/cgl-docker-lib
that referenced
this pull request
Aug 1, 2016
Picks up: * bigdatagenomics/quinine@a5cb6b0, fix for bigdatagenomics/quinine#34 * bigdatagenomics/quinine@be8a1b6, fix for bigdatagenomics/quinine#35, * Merge commit bigdatagenomics/quinine@2475aea * Force pushed update BD2KGenomics/toil-scripts@eed1ef8 to BD2KGenomics/toil-scripts#381.
cket
pushed a commit
to cket/cgl-docker-lib
that referenced
this pull request
Sep 7, 2016
Picks up: * bigdatagenomics/quinine@a5cb6b0, fix for bigdatagenomics/quinine#34 * bigdatagenomics/quinine@be8a1b6, fix for bigdatagenomics/quinine#35, * Merge commit bigdatagenomics/quinine@2475aea * Force pushed update BD2KGenomics/toil-scripts@eed1ef8 to BD2KGenomics/toil-scripts#381.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
5 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Builds on top of #351.