Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / PMCC-BioinformaticsCore/janis-bioinformatics issues and pull requests

#129 - Release v0.12.2

Pull Request - State: closed - Opened by rlupat over 1 year ago

#128 - Release v0.12.0

Pull Request - State: closed - Opened by GraceAHall over 1 year ago

#127 - Release v0.12.1

Pull Request - State: closed - Opened by rlupat over 1 year ago

#126 - Bugfix gatherfilesmultiqc

Pull Request - State: closed - Opened by rlupat over 1 year ago

#125 - remove the intermediate sample names for refiltering

Pull Request - State: closed - Opened by SebastianHollizeck over 2 years ago

#124 - mRNA expression pipeline related tools

Pull Request - State: closed - Opened by jiaan-yu almost 3 years ago

#123 - Merge master into oncopipe

Pull Request - State: closed - Opened by jiaan-yu almost 3 years ago

#122 - Add new tools to localise files, and fixes tools with stdout output

Pull Request - State: closed - Opened by jiaan-yu almost 3 years ago - 1 comment

#121 - Bug fix: correctly parse adapter/contaminant sequence from fastqc

Pull Request - State: closed - Opened by jiaan-yu almost 3 years ago

#120 - Add RNASeq Fusion Workflow related tools

Pull Request - State: closed - Opened by jiaan-yu about 3 years ago - 1 comment

#119 - Add required metadata to gatherfilesformultiqc

Pull Request - State: closed - Opened by rlupat about 3 years ago

#118 - Add tool RNASeqQC and minor fix

Pull Request - State: closed - Opened by jiaan-yu over 3 years ago

#117 - __doc__ of FastqcSingleScattered versions.py is None

Issue - State: open - Opened by kinow over 3 years ago - 1 comment

#116 - Add tool CircosPlot

Pull Request - State: closed - Opened by jiaan-yu over 3 years ago

#115 - Fix typos on README and python comments

Pull Request - State: closed - Opened by kinow over 3 years ago

#114 - Change samtools mpileup

Pull Request - State: closed - Opened by jiaan-yu over 3 years ago

#113 - Fix the output files matching of Manta

Pull Request - State: closed - Opened by jiaan-yu over 3 years ago

#112 - Release v0.12.0

Pull Request - State: closed - Opened by junyk over 3 years ago

#111 - Fix vardict filter

Pull Request - State: closed - Opened by jiaan-yu over 3 years ago

#110 - restore space between -R and its argument

Pull Request - State: closed - Opened by junyk over 3 years ago

#109 - Changes related to Nextflow implementation

Pull Request - State: closed - Opened by junyk over 3 years ago

#108 - Fixed a bug where freebayes would create the same variant twice

Pull Request - State: closed - Opened by SebastianHollizeck over 3 years ago - 1 comment

#107 - Remove split bam step from gatk calling

Pull Request - State: closed - Opened by jiaan-yu over 3 years ago - 1 comment

#106 - Set Bcftools concat input to UnionType

Pull Request - State: closed - Opened by jiaan-yu over 3 years ago - 1 comment

#105 - Reduce test files

Pull Request - State: closed - Opened by junyk over 3 years ago - 3 comments

#104 - upgrade to v0.11.1

Pull Request - State: closed - Opened by junyk over 3 years ago - 1 comment

#103 - Rename GenerateIntervalByChromosome

Pull Request - State: closed - Opened by jiaan-yu over 3 years ago - 1 comment

#102 - Add tool GenerateMantaConfig

Pull Request - State: closed - Opened by jiaan-yu over 3 years ago

#101 - Clean up and add new tools in bcftools

Pull Request - State: closed - Opened by jiaan-yu over 3 years ago

#100 - Unit test wgssomatic

Pull Request - State: closed - Opened by xinzhel97 over 3 years ago - 9 comments

#99 - Remove "chromNamesAreNumbers" option from VarDict - fix bug

Pull Request - State: closed - Opened by jiaan-yu over 3 years ago

#98 - Add gridss version 2.8.3

Pull Request - State: closed - Opened by jiaan-yu over 3 years ago

#97 - Include test data in subdirectories

Pull Request - State: closed - Opened by junyk almost 4 years ago

#96 - Gridss 2.10

Pull Request - State: closed - Opened by jiaan-yu almost 4 years ago - 1 comment

#95 - Unit test wgsgermline workflow

Pull Request - State: closed - Opened by xinzhel97 almost 4 years ago - 9 comments

#94 - Add facets and minor bug fixing wgs pipeline

Pull Request - State: closed - Opened by jiaan-yu almost 4 years ago - 1 comment

#93 - Add facets and bug fixing

Pull Request - State: closed - Opened by jiaan-yu almost 4 years ago
Labels: duplicate

#92 - Improving janis-bioinformatics structure

Issue - State: open - Opened by illusional about 4 years ago

#91 - Simplifying version definitions

Issue - State: open - Opened by illusional about 4 years ago

#90 - Refactor GATK4 tool IDS

Issue - State: open - Opened by illusional about 4 years ago

#89 - Test files

Pull Request - State: closed - Opened by junyk about 4 years ago - 1 comment

#88 - cleanup of spagetti code through inheritance

Pull Request - State: closed - Opened by SebastianHollizeck about 4 years ago - 1 comment

#87 - major restructure

Pull Request - State: closed - Opened by SebastianHollizeck about 4 years ago

#86 - update versions for tools

Pull Request - State: closed - Opened by SebastianHollizeck about 4 years ago

#85 - More generic lookup of test_data folder

Pull Request - State: closed - Opened by junyk about 4 years ago

#84 - Oncopipe variant calling update

Pull Request - State: closed - Opened by jiaan-yu about 4 years ago - 4 comments

#83 - Added tool metadata, added github actions hook, removed travis

Pull Request - State: closed - Opened by junyk about 4 years ago

#82 - V0.11.x

Pull Request - State: closed - Opened by illusional about 4 years ago - 1 comment

#81 - Unit tests for bioinformatics tool

Pull Request - State: closed - Opened by junyk about 4 years ago - 1 comment

#80 - Janis prepare

Pull Request - State: closed - Opened by illusional about 4 years ago

#79 - make stdout a text file

Pull Request - State: closed - Opened by drtconway over 4 years ago

#78 - Vep improvements

Pull Request - State: closed - Opened by drtconway over 4 years ago - 1 comment

#77 - moved to a more intuitive version of specifying max coverage per bam

Pull Request - State: closed - Opened by SebastianHollizeck over 4 years ago - 1 comment

#76 - Performance summary fix

Pull Request - State: closed - Opened by jiaan-yu over 4 years ago

#75 - Remove secondary alignment for the input bam

Pull Request - State: closed - Opened by jiaan-yu over 4 years ago

#74 - Gatk version fix

Pull Request - State: closed - Opened by jiaan-yu over 4 years ago

#73 - GATK4 tools version patch

Pull Request - State: closed - Opened by jiaan-yu over 4 years ago

#72 - Oncopipe

Pull Request - State: closed - Opened by jiaan-yu over 4 years ago

#70 - optimisations

Pull Request - State: closed - Opened by SebastianHollizeck over 4 years ago

#69 - Add testing framework

Pull Request - State: closed - Opened by illusional over 4 years ago

#68 - Replace PeterMacUtils version with 0.1.1

Pull Request - State: closed - Opened by jiaan-yu over 4 years ago - 2 comments

#67 - creating the latest versions for tools

Pull Request - State: closed - Opened by SebastianHollizeck over 4 years ago

#66 - Change reference type for a few tools

Pull Request - State: closed - Opened by SebastianHollizeck over 4 years ago

#65 - Fix gatk4 splitreads output

Pull Request - State: closed - Opened by jiaan-yu over 4 years ago - 1 comment

#64 - move to only fasta + fai

Pull Request - State: closed - Opened by SebastianHollizeck over 4 years ago

#63 - Bug fix in addbamstats

Pull Request - State: closed - Opened by jiaan-yu over 4 years ago

#62 - Add single fastqc to add directory output

Pull Request - State: closed - Opened by illusional over 4 years ago

#61 - Modify strelka somatic steps and minor bug fix

Pull Request - State: closed - Opened by jiaan-yu over 4 years ago

#60 - change output type to array of vcfs

Pull Request - State: closed - Opened by SebastianHollizeck over 4 years ago

#59 - Add optional somaticSV to manta out

Pull Request - State: closed - Opened by illusional over 4 years ago - 1 comment

#57 - Bcc tools

Pull Request - State: closed - Opened by illusional over 4 years ago

#56 - Add subread

Pull Request - State: closed - Opened by jiaan-yu over 4 years ago

#55 - Upstream molpath

Pull Request - State: closed - Opened by jiaan-yu over 4 years ago

#54 - Add various tools + fix existing pipelines

Pull Request - State: closed - Opened by illusional over 4 years ago - 1 comment

#53 - Molpath

Pull Request - State: closed - Opened by jiaan-yu over 4 years ago

#52 - Change CombineVariant version to 0.0.8

Pull Request - State: closed - Opened by jiaan-yu over 4 years ago

#51 - Fix gridss bam output secondary file matching

Pull Request - State: closed - Opened by jiaan-yu over 4 years ago

#50 - Molpath version update

Pull Request - State: closed - Opened by jiaan-yu over 4 years ago

#49 - Add whisper aligner

Pull Request - State: closed - Opened by drtconway over 4 years ago - 2 comments

#48 - fix import so janis inputs works.

Pull Request - State: closed - Opened by drtconway over 4 years ago

#47 - Performance summary bed file fix

Pull Request - State: closed - Opened by jiaan-yu over 4 years ago

#46 - fixed version typo

Pull Request - State: closed - Opened by SebastianHollizeck over 4 years ago

#45 - Sebastian drawsontoolkit minorfixes

Pull Request - State: closed - Opened by illusional over 4 years ago

#44 - Molpath PHCP

Pull Request - State: closed - Opened by jiaan-yu over 4 years ago - 2 comments

#43 - Seqliner

Pull Request - State: closed - Opened by jiaan-yu over 4 years ago - 2 comments

#42 - SamtoolsFaidx missing

Issue - State: closed - Opened by drtconway over 4 years ago - 1 comment

#41 - Make mutect2 normal inputs optional per spec

Pull Request - State: closed - Opened by illusional over 4 years ago

#40 - Gatk4Mutect2 usage

Issue - State: closed - Opened by drtconway over 4 years ago - 2 comments

#39 - add a basic integration of kallisto.

Pull Request - State: closed - Opened by drtconway over 4 years ago - 1 comment

#38 - Oncopipe tools

Pull Request - State: closed - Opened by illusional over 4 years ago

#37 - Add Facets and Sequenza

Pull Request - State: closed - Opened by evan-wehi over 4 years ago - 1 comment

#36 - Add autogenerated GATK tool wrappers

Pull Request - State: closed - Opened by illusional over 4 years ago

#35 - Request to merge with jiaan's dev branch

Pull Request - State: closed - Opened by jiaan-yu almost 5 years ago - 3 comments

#34 - Output BAM doesn't get copied.

Issue - State: closed - Opened by drtconway almost 5 years ago - 2 comments

#33 - Comment out the unused temporaryOutputs output on samtoolssort

Pull Request - State: closed - Opened by illusional almost 5 years ago

#32 - SamToolsSort outputs

Issue - State: closed - Opened by drtconway almost 5 years ago - 1 comment

#31 - Add region argument to SamtoolsView

Pull Request - State: closed - Opened by illusional almost 5 years ago

#29 - Star branch Update

Pull Request - State: closed - Opened by jiaan-yu almost 5 years ago