hammerlab/biokepi issues and pull requests

#100 - Specify patch for genomes

Issue - State: closed - Opened by ihodes about 9 years ago - 6 comments

#100 - Specify patch for genomes

Issue - State: closed - Opened by ihodes about 9 years ago - 6 comments

#99 - Reimplement other people's pipelines

Issue - State: open - Opened by smondet about 9 years ago

#99 - Reimplement other people's pipelines

Issue - State: open - Opened by smondet about 9 years ago

#98 - Split the module Run_environment

Pull Request - State: closed - Opened by smondet about 9 years ago - 1 comment

#98 - Split the module Run_environment

Pull Request - State: closed - Opened by smondet about 9 years ago - 1 comment

#97 - Add parameters to Gatk's Bqsr

Pull Request - State: closed - Opened by ihodes about 9 years ago

#97 - Add parameters to Gatk's Bqsr

Pull Request - State: closed - Opened by ihodes about 9 years ago

#96 - Document pipeline.ml

Issue - State: closed - Opened by ihodes about 9 years ago - 1 comment

#96 - Document pipeline.ml

Issue - State: closed - Opened by ihodes about 9 years ago - 1 comment

#95 - GATK BQSR should take arguments

Issue - State: closed - Opened by ihodes about 9 years ago

#95 - GATK BQSR should take arguments

Issue - State: closed - Opened by ihodes about 9 years ago

#94 - Remove excess fmt string in IndelRealigner args

Pull Request - State: closed - Opened by ihodes about 9 years ago

#94 - Remove excess fmt string in IndelRealigner args

Pull Request - State: closed - Opened by ihodes about 9 years ago

#93 - Allow MuTect to take parameters

Pull Request - State: closed - Opened by ihodes about 9 years ago

#93 - Allow MuTect to take parameters

Pull Request - State: closed - Opened by ihodes about 9 years ago

#92 - Add spaces around args in GATK indel_realigner

Pull Request - State: closed - Opened by ihodes about 9 years ago

#92 - Add spaces around args in GATK indel_realigner

Pull Request - State: closed - Opened by ihodes about 9 years ago

#91 - Allow Gatk.indel_realigner to be configured

Pull Request - State: closed - Opened by ihodes about 9 years ago - 1 comment

#91 - Allow Gatk.indel_realigner to be configured

Pull Request - State: closed - Opened by ihodes about 9 years ago - 1 comment

#90 - Mutect should take parameters like Strelka does

Issue - State: closed - Opened by ihodes about 9 years ago - 1 comment
Labels: enhancement

#90 - Mutect should take parameters like Strelka does

Issue - State: closed - Opened by ihodes about 9 years ago - 1 comment
Labels: enhancement

#89 - Make COSMIC optional for Mutect

Issue - State: closed - Opened by ihodes about 9 years ago
Labels: bug

#89 - Make COSMIC optional for Mutect

Issue - State: closed - Opened by ihodes about 9 years ago
Labels: bug

#88 - Create a repository for datasets/revive the Dataset module

Issue - State: open - Opened by ihodes about 9 years ago - 2 comments
Labels: enhancement, question

#88 - Create a repository for datasets/revive the Dataset module

Issue - State: open - Opened by ihodes about 9 years ago - 2 comments
Labels: enhancement, question

#87 - No more option condition

Pull Request - State: closed - Opened by rleonid about 9 years ago - 1 comment

#87 - No more option condition

Pull Request - State: closed - Opened by rleonid about 9 years ago - 1 comment

#86 - Remove option wrapper around is_done Condition

Issue - State: closed - Opened by rleonid about 9 years ago - 1 comment

#86 - Remove option wrapper around is_done Condition

Issue - State: closed - Opened by rleonid about 9 years ago - 1 comment

#85 - Make reference-build handling more extensible

Issue - State: closed - Opened by smondet about 9 years ago - 2 comments
Labels: help wanted

#85 - Make reference-build handling more extensible

Issue - State: closed - Opened by smondet about 9 years ago - 2 comments
Labels: help wanted

#84 - `Pipeline.t` → dot (or some other display-friendly format)

Issue - State: closed - Opened by smondet about 9 years ago
Labels: help wanted

#84 - `Pipeline.t` → dot (or some other display-friendly format)

Issue - State: closed - Opened by smondet about 9 years ago
Labels: help wanted

#83 - Add developer files

Pull Request - State: closed - Opened by rleonid about 9 years ago

#83 - Add developer files

Pull Request - State: closed - Opened by rleonid about 9 years ago

#82 - Pass processors through to Yarn/scheduler to be a "good citizen"

Issue - State: closed - Opened by ihodes about 9 years ago - 1 comment

#82 - Pass processors through to Yarn/scheduler to be a "good citizen"

Issue - State: closed - Opened by ihodes about 9 years ago - 1 comment

#81 - Re-enable oredoc documentation generation

Pull Request - State: closed - Opened by rleonid about 9 years ago

#81 - Re-enable oredoc documentation generation

Pull Request - State: closed - Opened by rleonid about 9 years ago

#80 - Return the oredoc document generation

Issue - State: closed - Opened by rleonid about 9 years ago

#80 - Return the oredoc document generation

Issue - State: closed - Opened by rleonid about 9 years ago

#79 - Reorganizing modules into pipelines

Issue - State: closed - Opened by arahuja about 9 years ago - 4 comments

#79 - Reorganizing modules into pipelines

Issue - State: closed - Opened by arahuja about 9 years ago - 4 comments

#78 - Test tool installations on different architectures

Issue - State: open - Opened by smondet about 9 years ago

#78 - Test tool installations on different architectures

Issue - State: open - Opened by smondet about 9 years ago

#77 - Kallisto transcript quantification tool

Pull Request - State: closed - Opened by arahuja about 9 years ago

#77 - Kallisto transcript quantification tool

Pull Request - State: closed - Opened by arahuja about 9 years ago

#76 - Add sorting dependency to cufflinks

Pull Request - State: closed - Opened by arahuja about 9 years ago

#76 - Add sorting dependency to cufflinks

Pull Request - State: closed - Opened by arahuja about 9 years ago

#75 - Add documentation (2nd try)

Pull Request - State: closed - Opened by rleonid about 9 years ago

#75 - Add documentation (2nd try)

Pull Request - State: closed - Opened by rleonid about 9 years ago

#74 - Clear up the README

Pull Request - State: closed - Opened by rleonid about 9 years ago

#74 - Clear up the README

Pull Request - State: closed - Opened by rleonid about 9 years ago

#73 - Add documentation

Pull Request - State: closed - Opened by rleonid about 9 years ago

#73 - Add documentation

Pull Request - State: closed - Opened by rleonid about 9 years ago

#72 - Generate online API documentation

Issue - State: closed - Opened by rleonid about 9 years ago - 1 comment

#72 - Generate online API documentation

Issue - State: closed - Opened by rleonid about 9 years ago - 1 comment

#71 - Example script for local somatic variant calling

Issue - State: closed - Opened by iskandr about 9 years ago - 3 comments

#71 - Example script for local somatic variant calling

Issue - State: closed - Opened by iskandr about 9 years ago - 3 comments

#70 - Add mm9 and mm10 mouse genomes

Issue - State: open - Opened by iskandr about 9 years ago - 1 comment

#70 - Add mm9 and mm10 mouse genomes

Issue - State: open - Opened by iskandr about 9 years ago - 1 comment

#69 - Add the MOSAIK aligner

Pull Request - State: closed - Opened by arahuja about 9 years ago

#69 - Add the MOSAIK aligner

Pull Request - State: closed - Opened by arahuja about 9 years ago

#68 - Ketrew 2.0.0 and more hooks to compile pipelines

Pull Request - State: closed - Opened by smondet over 9 years ago

#68 - Ketrew 2.0.0 and more hooks to compile pipelines

Pull Request - State: closed - Opened by smondet over 9 years ago

#67 - add filter_reads_with_N_cigar to GATK HC

Pull Request - State: closed - Opened by arahuja over 9 years ago - 4 comments

#67 - add filter_reads_with_N_cigar to GATK HC

Pull Request - State: closed - Opened by arahuja over 9 years ago - 4 comments

#66 - Fix STAR output path

Pull Request - State: closed - Opened by arahuja over 9 years ago

#66 - Fix STAR output path

Pull Request - State: closed - Opened by arahuja over 9 years ago

#65 - Add md tag to star output

Pull Request - State: closed - Opened by arahuja over 9 years ago - 1 comment

#65 - Add md tag to star output

Pull Request - State: closed - Opened by arahuja over 9 years ago - 1 comment

#64 - add mdtag to star output (and any other aligners that don't do this already)

Issue - State: closed - Opened by timodonnell over 9 years ago

#64 - add mdtag to star output (and any other aligners that don't do this already)

Issue - State: closed - Opened by timodonnell over 9 years ago

#63 - mutect dbsnp file gotchas

Issue - State: open - Opened by timodonnell over 9 years ago

#63 - mutect dbsnp file gotchas

Issue - State: open - Opened by timodonnell over 9 years ago

#62 - document Common.ml

Issue - State: open - Opened by timodonnell over 9 years ago

#62 - document Common.ml

Issue - State: open - Opened by timodonnell over 9 years ago

#61 - Adding HISAT RNA aligner

Pull Request - State: closed - Opened by arahuja over 9 years ago

#61 - Adding HISAT RNA aligner

Pull Request - State: closed - Opened by arahuja over 9 years ago

#60 - Remove equivalence from single end

Pull Request - State: closed - Opened by arahuja over 9 years ago - 1 comment

#60 - Remove equivalence from single end

Pull Request - State: closed - Opened by arahuja over 9 years ago - 1 comment

#59 - Remove single end todo

Pull Request - State: closed - Opened by arahuja over 9 years ago

#59 - Remove single end todo

Pull Request - State: closed - Opened by arahuja over 9 years ago

#58 - Add stringtie and cufflinks modules

Pull Request - State: closed - Opened by arahuja over 9 years ago

#58 - Add stringtie and cufflinks modules

Pull Request - State: closed - Opened by arahuja over 9 years ago

#57 - output compressed VCFs from variant callers

Issue - State: closed - Opened by timodonnell over 9 years ago - 3 comments

#57 - output compressed VCFs from variant callers

Issue - State: closed - Opened by timodonnell over 9 years ago - 3 comments

#56 - Improve file naming

Issue - State: open - Opened by smondet over 9 years ago

#56 - Improve file naming

Issue - State: open - Opened by smondet over 9 years ago

#55 - Add STAR RNA aligner

Pull Request - State: closed - Opened by arahuja over 9 years ago

#55 - Add STAR RNA aligner

Pull Request - State: closed - Opened by arahuja over 9 years ago

#54 - Name bam pair after tumor file

Pull Request - State: closed - Opened by arahuja over 9 years ago - 1 comment

#54 - Name bam pair after tumor file

Pull Request - State: closed - Opened by arahuja over 9 years ago - 1 comment

#53 - Fix hg18 dbSNP url

Pull Request - State: closed - Opened by arahuja over 9 years ago

#53 - Fix hg18 dbSNP url

Pull Request - State: closed - Opened by arahuja over 9 years ago

#52 - Optionally clean-up intermediary pipeline files

Issue - State: open - Opened by smondet over 9 years ago

#52 - Optionally clean-up intermediary pipeline files

Issue - State: open - Opened by smondet over 9 years ago

#51 - Specify the tmpdir for java as well for picard

Pull Request - State: closed - Opened by arahuja over 9 years ago - 1 comment

#51 - Specify the tmpdir for java as well for picard

Pull Request - State: closed - Opened by arahuja over 9 years ago - 1 comment

GitHub / hammerlab/biokepi issues and pull requests