BD2KGenomics/toil-lib issues and pull requests

#109 - Add Deca (resolves #108)

Pull Request - State: open - Opened by fnothaft about 7 years ago - 1 comment

#108 - Add DECA method in toil_lib.tools.spark_tools

Issue - State: closed - Opened by fnothaft about 7 years ago

#107 - Add benchmarking mode (resolves #101)

Pull Request - State: open - Opened by fnothaft about 7 years ago

#106 - Misc ADAM recompute upgrades (resolves #90)

Pull Request - State: open - Opened by fnothaft about 7 years ago - 1 comment

#105 - Added bowtie2 and SNAP aligners (resolves #102)

Pull Request - State: open - Opened by fnothaft about 7 years ago

#104 - Add sambamba index (resolves #103)

Pull Request - State: closed - Opened by fnothaft about 7 years ago

#103 - Add Sambama index

Issue - State: closed - Opened by fnothaft about 7 years ago

#102 - Add two new aligners

Issue - State: open - Opened by fnothaft about 7 years ago

#102 - Add two new aligners

Issue - State: open - Opened by fnothaft about 7 years ago

#101 - Add benchmarking mode to all tools

Issue - State: open - Opened by fnothaft about 7 years ago

#101 - Add benchmarking mode to all tools

Issue - State: open - Opened by fnothaft about 7 years ago

#100 - Make docker image parametrizable for all tools

Issue - State: open - Opened by fnothaft about 7 years ago

#100 - Make docker image parametrizable for all tools

Issue - State: open - Opened by fnothaft about 7 years ago

#99 - Added variant callers for benchmarking (resolves #97)

Pull Request - State: open - Opened by fnothaft about 7 years ago - 3 comments

#98 - Fix typo in samblaster parameter name

Pull Request - State: closed - Opened by fnothaft about 7 years ago

#97 - Add new variant callers to benchmark against

Issue - State: open - Opened by fnothaft about 7 years ago
Labels: enhancement

#97 - Add new variant callers to benchmark against

Issue - State: open - Opened by fnothaft about 7 years ago
Labels: enhancement

#96 - Added alternate sort and duplicate marking tools (resolves #95)

Pull Request - State: closed - Opened by fnothaft about 7 years ago - 3 comments

#96 - Added alternate sort and duplicate marking tools (resolves #95)

Pull Request - State: closed - Opened by fnothaft about 7 years ago - 3 comments

#95 - Add sambamba, samblaster

Issue - State: closed - Opened by fnothaft about 7 years ago

#95 - Add sambamba, samblaster

Issue - State: closed - Opened by fnothaft about 7 years ago

#94 - Instrument GATK functions (resolves #93)

Pull Request - State: closed - Opened by fnothaft about 7 years ago - 3 comments

#94 - Instrument GATK functions (resolves #93)

Pull Request - State: closed - Opened by fnothaft about 7 years ago - 3 comments

#93 - Log timings to master for GATK pipeline

Issue - State: closed - Opened by fnothaft about 7 years ago

#93 - Log timings to master for GATK pipeline

Issue - State: closed - Opened by fnothaft about 7 years ago

#92 - Add sort option to STAR (resolves #91)

Pull Request - State: closed - Opened by jvivian over 7 years ago

#92 - Add sort option to STAR (resolves #91)

Pull Request - State: closed - Opened by jvivian over 7 years ago

#91 - Add sort option to STAR

Issue - State: closed - Opened by jvivian over 7 years ago

#91 - Add sort option to STAR

Issue - State: closed - Opened by jvivian over 7 years ago

#90 - ADAM recompute upgrades

Issue - State: open - Opened by fnothaft over 7 years ago

#89 - Remove dockercall (resolves #68)

Pull Request - State: closed - Opened by fnothaft over 7 years ago - 13 comments

#88 - Add fusion output from Kallisto (resolves #87)

Pull Request - State: closed - Opened by jvivian over 7 years ago - 1 comment

#88 - Add fusion output from Kallisto (resolves #87)

Pull Request - State: closed - Opened by jvivian over 7 years ago - 1 comment

#87 - Add fusion results to Kallisto output

Issue - State: closed - Opened by jvivian over 7 years ago

#87 - Add fusion results to Kallisto output

Issue - State: closed - Opened by jvivian over 7 years ago

#86 - Revert "Within KeepPairs" to "Within" (resolves #85)

Pull Request - State: closed - Opened by jvivian over 7 years ago - 1 comment

#86 - Revert "Within KeepPairs" to "Within" (resolves #85)

Pull Request - State: closed - Opened by jvivian over 7 years ago - 1 comment

#85 - Revert Within KeepPairs to Within in STAR

Issue - State: closed - Opened by jvivian over 7 years ago

#85 - Revert Within KeepPairs to Within in STAR

Issue - State: closed - Opened by jvivian over 7 years ago

#84 - Add splice junction from STAR to output (resolves #83)

Pull Request - State: closed - Opened by jvivian over 7 years ago

#84 - Add splice junction from STAR to output (resolves #83)

Pull Request - State: closed - Opened by jvivian over 7 years ago

#83 - return rnaSJ.out.tab for STAR

Issue - State: closed - Opened by jvivian over 7 years ago

#83 - return rnaSJ.out.tab for STAR

Issue - State: closed - Opened by jvivian over 7 years ago

#82 - FileIOStore symlinks don't work with docker

Issue - State: closed - Opened by glennhickey over 7 years ago - 1 comment

#82 - FileIOStore symlinks don't work with docker

Issue - State: closed - Opened by glennhickey over 7 years ago - 1 comment

#81 - S3IOStore cannot transfer big files

Issue - State: closed - Opened by glennhickey over 7 years ago - 2 comments

#81 - S3IOStore cannot transfer big files

Issue - State: closed - Opened by glennhickey over 7 years ago - 2 comments

#80 - Support piped commands in docker_call

Issue - State: closed - Opened by glennhickey over 7 years ago - 2 comments

#80 - Support piped commands in docker_call

Issue - State: closed - Opened by glennhickey over 7 years ago - 2 comments

#79 - Move jpfeil/oncotator:1.9 to cgl-docker-lib

Issue - State: open - Opened by jvivian over 7 years ago

#79 - Move jpfeil/oncotator:1.9 to cgl-docker-lib

Issue - State: open - Opened by jvivian over 7 years ago

#78 - Remove dockercall (resolves #68)

Pull Request - State: open - Opened by jvivian over 7 years ago - 16 comments
Labels: in progress

#78 - Remove dockercall (resolves #68)

Pull Request - State: open - Opened by jvivian over 7 years ago - 16 comments
Labels: in progress

#77 - Fix rsem_postprocess typo (resolves #76)

Pull Request - State: closed - Opened by jvivian over 7 years ago - 1 comment

#76 - Fix typo in rsem_postprocess

Issue - State: closed - Opened by jvivian over 7 years ago

#76 - Fix typo in rsem_postprocess

Issue - State: closed - Opened by jvivian over 7 years ago

#75 - Remove mutable=True (resolves #74)

Pull Request - State: closed - Opened by jvivian over 7 years ago - 1 comment

#75 - Remove mutable=True (resolves #74)

Pull Request - State: closed - Opened by jvivian over 7 years ago - 1 comment

#74 - Remove mutable=True from toil-lib

Issue - State: closed - Opened by jvivian over 7 years ago

#74 - Remove mutable=True from toil-lib

Issue - State: closed - Opened by jvivian over 7 years ago

#73 - Release 1.1.2

Issue - State: closed - Opened by jvivian over 7 years ago

#73 - Release 1.1.2

Issue - State: closed - Opened by jvivian over 7 years ago

#72 - Refactor rsem postprocess (resolves #70, resolves #71)

Pull Request - State: closed - Opened by jvivian over 7 years ago

#72 - Refactor rsem postprocess (resolves #70, resolves #71)

Pull Request - State: closed - Opened by jvivian over 7 years ago

#71 - Refactor rsem_postprocess

Issue - State: closed - Opened by jvivian over 7 years ago - 1 comment

#70 - Update to quay.io tools in run_rsem_postprocess

Issue - State: closed - Opened by jvivian over 7 years ago

#69 - Add support for Redwood

Issue - State: open - Opened by jvivian over 7 years ago - 2 comments

#69 - Add support for Redwood

Issue - State: open - Opened by jvivian over 7 years ago - 2 comments

#68 - Remove docker_call

Issue - State: closed - Opened by jvivian almost 8 years ago - 3 comments

#67 - 1.1.1 Release

Issue - State: closed - Opened by jvivian almost 8 years ago

#67 - 1.1.1 Release

Issue - State: closed - Opened by jvivian almost 8 years ago

#66 - Add --limitBAMsortRAM argument

Pull Request - State: closed - Opened by jvivian almost 8 years ago

#66 - Add --limitBAMsortRAM argument

Pull Request - State: closed - Opened by jvivian almost 8 years ago

#65 - not pip-installable on cgcloud toil-box-templated toil-leader?

Issue - State: closed - Opened by ArtRand almost 8 years ago - 1 comment

#65 - not pip-installable on cgcloud toil-box-templated toil-leader?

Issue - State: closed - Opened by ArtRand almost 8 years ago - 1 comment

#64 - Make indel realignment optional (resolves #63)

Pull Request - State: closed - Opened by jpfeil almost 8 years ago - 2 comments

#64 - Make indel realignment optional (resolves #63)

Pull Request - State: closed - Opened by jpfeil almost 8 years ago - 2 comments

#63 - Make indel realignment optional

Issue - State: closed - Opened by jpfeil almost 8 years ago

#63 - Make indel realignment optional

Issue - State: closed - Opened by jpfeil almost 8 years ago

#62 - Add mark secondary option to run_bwakit

Pull Request - State: closed - Opened by jpfeil almost 8 years ago - 3 comments

#62 - Add mark secondary option to run_bwakit

Pull Request - State: closed - Opened by jpfeil almost 8 years ago - 3 comments

#61 - Add mark secondary option to run_bwakit

Issue - State: open - Opened by jpfeil almost 8 years ago

#60 - Add documentation

Pull Request - State: open - Opened by almussel almost 8 years ago - 1 comment
Labels: needs work, in progress

#60 - Add documentation

Pull Request - State: open - Opened by almussel almost 8 years ago - 1 comment
Labels: needs work, in progress

#59 - Add manual (Sphinx documentation)

Issue - State: open - Opened by hannes-ucsc almost 8 years ago - 2 comments

#59 - Add manual (Sphinx documentation)

Issue - State: open - Opened by hannes-ucsc almost 8 years ago - 2 comments

#58 - Suppress mock_mode for download of intermediate files

Pull Request - State: closed - Opened by almussel almost 8 years ago - 2 comments

#58 - Suppress mock_mode for download of intermediate files

Pull Request - State: closed - Opened by almussel almost 8 years ago - 2 comments

#57 - Mock_mode prevents downloads of intermediate files

Issue - State: closed - Opened by almussel almost 8 years ago

#57 - Mock_mode prevents downloads of intermediate files

Issue - State: closed - Opened by almussel almost 8 years ago

#56 - Use parse_version (resolves #55)

Pull Request - State: closed - Opened by cket almost 8 years ago

#56 - Use parse_version (resolves #55)

Pull Request - State: closed - Opened by cket almost 8 years ago

#55 - Use parse_version

Issue - State: closed - Opened by cket almost 8 years ago

#55 - Use parse_version

Issue - State: closed - Opened by cket almost 8 years ago

#54 - Add unit tests for tools

Issue - State: open - Opened by cket almost 8 years ago

#54 - Add unit tests for tools

Issue - State: open - Opened by cket almost 8 years ago

#53 - Update docker call invocations (resolves #44)

Pull Request - State: closed - Opened by cket almost 8 years ago - 2 comments

#53 - Update docker call invocations (resolves #44)

Pull Request - State: closed - Opened by cket almost 8 years ago - 2 comments

#52 - Add defer to inferior filestore

Issue - State: closed - Opened by arkal almost 8 years ago - 1 comment

#52 - Add defer to inferior filestore

Issue - State: closed - Opened by arkal almost 8 years ago - 1 comment

GitHub / BD2KGenomics/toil-lib issues and pull requests