Ecosyste.ms: Issues

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

GitHub / mskcc/tempo issues and pull requests

#1015 - Enhancement/interval channel

Pull Request - State: open - Opened by anoronh4 3 months ago

#1014 - conpair channel bug

Issue - State: closed - Opened by anoronh4 7 months ago

#1013 - fix conpair channel

Pull Request - State: closed - Opened by anoronh4 7 months ago - 1 comment

#1012 - Feature/upgrade delly v126

Pull Request - State: open - Opened by anoronh4 8 months ago - 1 comment

#1011 - replace or upgrade delly

Issue - State: open - Opened by anoronh4 9 months ago
Labels: somatic analysis

#1010 - Add assay type to MultiQC output.

Issue - State: open - Opened by price0416 9 months ago
Labels: enhancement, qc

#1009 - use Channel.interval() factory instead of watchPath

Issue - State: open - Opened by anoronh4 9 months ago - 1 comment
Labels: backburner

#1008 - emit original quals

Pull Request - State: closed - Opened by anoronh4 10 months ago - 1 comment

#1007 - clean up ngi-genomes folder

Issue - State: open - Opened by anoronh4 11 months ago

#1006 - update test-data link for travis

Pull Request - State: closed - Opened by anoronh4 11 months ago

#1005 - removed deprecated pipeline.nf mentions from docs

Pull Request - State: closed - Opened by anoronh4 11 months ago - 1 comment

#1004 - remove pipeline.nf from docs for dsl2

Issue - State: closed - Opened by anoronh4 11 months ago
Labels: bug

#1003 - enabled storeDir for dsl2

Pull Request - State: closed - Opened by anoronh4 about 1 year ago

#1001 - allow storeDir for RunBQSR

Pull Request - State: open - Opened by anoronh4 about 1 year ago - 1 comment

#1000 - storeDir option doesn't work for all modules

Issue - State: open - Opened by anoronh4 about 1 year ago - 1 comment

#999 - update multiqc

Issue - State: open - Opened by anoronh4 about 1 year ago

#998 - Broken links in documentation

Issue - State: closed - Opened by johnoooh about 1 year ago

#997 - Improvement for cohort multiqc report html

Issue - State: open - Opened by gongyixiao about 1 year ago

#996 - Merge master hotfix back into develop

Pull Request - State: closed - Opened by anoronh4 about 1 year ago - 1 comment

#995 - update netlify documentation link

Pull Request - State: closed - Opened by anoronh4 about 1 year ago - 1 comment

#993 - fix empty bedpe

Pull Request - State: closed - Opened by anoronh4 about 1 year ago

#992 - update pipeline DAG visualization in documentation

Issue - State: open - Opened by anoronh4 over 1 year ago

#991 - Merge hotfix/1.4.4 back into develop

Pull Request - State: closed - Opened by anoronh4 over 1 year ago - 1 comment

#990 - Hotfix/1.4.4

Pull Request - State: closed - Opened by anoronh4 over 1 year ago - 1 comment

#989 - lohhla read.table bug

Issue - State: closed - Opened by anoronh4 over 1 year ago

#988 - Facets output incompatible with Facets Preview

Issue - State: closed - Opened by anoronh4 over 1 year ago - 1 comment

#987 - Fixed facets zygosity annotation of maf

Pull Request - State: closed - Opened by anoronh4 over 1 year ago - 1 comment

#985 - define intermediates_dir for rmarkdown rendering

Pull Request - State: closed - Opened by anoronh4 almost 2 years ago

#984 - Bug with biocircos plotting

Issue - State: closed - Opened by anoronh4 almost 2 years ago

#983 - Fix malformed Strelka VCFs

Pull Request - State: closed - Opened by anoronh4 almost 2 years ago - 1 comment

#982 - Remove unnecessary files from SvABA published files

Issue - State: open - Opened by anoronh4 almost 2 years ago - 2 comments
Labels: bug

#981 - Bugfix/shorten combine mutect2 vcf cmd

Pull Request - State: closed - Opened by gongyixiao almost 2 years ago
Labels: bug

#980 - bugfix/ lohhla should not turn onn mutsig subworkflow

Pull Request - State: closed - Opened by gongyixiao almost 2 years ago - 1 comment
Labels: bug

#979 - Bugfix/workflow logic issues

Pull Request - State: closed - Opened by anoronh4 about 2 years ago - 1 comment

#978 - nextflow updates causing errors in execution

Issue - State: open - Opened by anoronh4 about 2 years ago - 3 comments
Labels: bug

#977 - ClusterSV and SVSignature need to handle empty input bedpe

Issue - State: closed - Opened by gongyixiao over 2 years ago
Labels: bug

#976 - SomaticCombineMutect2Vcf force sample name override header

Issue - State: open - Opened by gongyixiao over 2 years ago
Labels: enhancement

#975 - minor issues in logic for dsl2

Issue - State: closed - Opened by anoronh4 over 2 years ago
Labels: bug

#973 - Dsl2/documentation updates

Pull Request - State: closed - Opened by price0416 over 2 years ago - 1 comment

#972 - Dsl2/enhancement/wgs sv

Pull Request - State: closed - Opened by anoronh4 over 2 years ago

#971 - updated docs for enhanced SV workflow

Pull Request - State: closed - Opened by anoronh4 over 2 years ago

#970 - Simplified target/bait inputs

Pull Request - State: open - Opened by anoronh4 over 2 years ago - 1 comment

#969 - Dsl2/enhancement/sv sigs

Pull Request - State: closed - Opened by anoronh4 over 2 years ago - 3 comments
Labels: somatic analysis

#968 - add custom read support filters in Delly and Manta Somatic calling

Pull Request - State: closed - Opened by anoronh4 over 2 years ago - 1 comment
Labels: enhancement, somatic analysis

#967 - Zygosity annotation of mutations should be done with hisens rather than purity

Issue - State: open - Opened by anoronh4 over 2 years ago - 1 comment
Labels: bug

#966 - Dsl2/merge any sv caller

Pull Request - State: closed - Opened by anoronh4 over 2 years ago
Labels: enhancement

#965 - Dsl2/filter sv blacklist

Pull Request - State: closed - Opened by anoronh4 over 2 years ago - 3 comments
Labels: enhancement

#964 - Optimize this line using wild card to shorten the printed command.

Issue - State: closed - Opened by gongyixiao over 2 years ago
Labels: enhancement, backburner

#963 - bugfix for single bam input into MergeBamsAndMarkDuplicates

Pull Request - State: closed - Opened by anoronh4 almost 3 years ago
Labels: bug, alignment

#962 - associate errorStrategy with maxRetries

Pull Request - State: closed - Opened by gongyixiao almost 3 years ago
Labels: bug

#961 - fix tag warning

Pull Request - State: closed - Opened by gongyixiao almost 3 years ago
Labels: bug

#960 - Enhancement/bam2fastq

Pull Request - State: open - Opened by gongyixiao almost 3 years ago - 2 comments
Labels: enhancement

#959 - Germline Maf PublishDir fix

Pull Request - State: closed - Opened by gongyixiao almost 3 years ago
Labels: bug

#958 - Bugfix - HsMetrics Input for WGS

Pull Request - State: closed - Opened by anoronh4 almost 3 years ago

#957 - SampleRunMultiQC not running for WGS mode

Issue - State: closed - Opened by gongyixiao almost 3 years ago - 1 comment
Labels: bug

#956 - Dsl2/feature/svaba brass

Pull Request - State: closed - Opened by anoronh4 almost 3 years ago - 1 comment

#955 - fix bam size calculation issue

Pull Request - State: closed - Opened by gongyixiao almost 3 years ago
Labels: bug

#953 - QcAlfred bug

Issue - State: closed - Opened by anoronh4 almost 3 years ago
Labels: bug

#952 - MergeBamsAndMarkDuplicates resource allocation wrong.

Issue - State: closed - Opened by gongyixiao almost 3 years ago
Labels: bug

#948 - add facets base image to tempo repo

Pull Request - State: closed - Opened by anoronh4 almost 3 years ago

#947 - Original quality scores are not kept in bams after BQSR

Issue - State: closed - Opened by anoronh4 almost 3 years ago - 1 comment
Labels: backburner, alignment

#944 - Dsl2/feature/hrdetect

Pull Request - State: closed - Opened by anoronh4 almost 3 years ago

#939 - facets-suite-preview Docker base image origin undocumented.

Issue - State: closed - Opened by gongyixiao about 3 years ago - 1 comment
Labels: question

#936 - Update oncoKB annotator version

Issue - State: open - Opened by gongyixiao about 3 years ago - 1 comment
Labels: enhancement

#928 - Maf files from GenomeNexus

Issue - State: open - Opened by price0416 about 3 years ago - 1 comment
Labels: enhancement

#927 - add cdna contamination calculation

Pull Request - State: closed - Opened by anoronh4 over 3 years ago - 1 comment
Labels: qc

#926 - calculate cdna contamination

Issue - State: closed - Opened by anoronh4 over 3 years ago
Labels: enhancement

#922 - Rescue mutations that are oncogenic at 2% frequency

Issue - State: open - Opened by anoronh4 over 3 years ago - 1 comment
Labels: somatic analysis

#916 - Mutect2 column is enforced in germline calls even though mutect is not used

Issue - State: open - Opened by anoronh4 over 3 years ago - 1 comment
Labels: bug

#915 - revise normal depth cutoff for variants

Issue - State: open - Opened by anoronh4 over 3 years ago - 1 comment
Labels: enhancement

#905 - Feature/ascat

Pull Request - State: closed - Opened by anoronh4 over 3 years ago
Labels: enhancement, somatic analysis

#903 - error in `GermlineCombineChannel`

Issue - State: open - Opened by anoronh4 over 3 years ago - 3 comments
Labels: bug, backburner, germline analysis

#894 - main development branch for WGS SV

Pull Request - State: closed - Opened by anoronh4 over 3 years ago
Labels: somatic analysis

#893 - Feature/create pon

Pull Request - State: open - Opened by anoronh4 almost 4 years ago - 1 comment

#892 - change input bam names of RunLOHHLA/QcQualimap/CollectHsMetrics

Issue - State: open - Opened by anoronh4 almost 4 years ago - 2 comments
Labels: bug, backburner

#891 - Publish unfiltered mutation vcf

Issue - State: closed - Opened by gongyixiao almost 4 years ago - 2 comments
Labels: enhancement, somatic analysis

#887 - error in `SomaticCombineChannel`

Issue - State: closed - Opened by anoronh4 almost 4 years ago - 7 comments
Labels: bug, backburner, somatic analysis

#862 - Feature/brass

Pull Request - State: closed - Opened by anoronh4 about 4 years ago - 1 comment

#861 - Feature/SvABA

Pull Request - State: closed - Opened by stevekm about 4 years ago - 2 comments

#859 - Updated testing

Pull Request - State: closed - Opened by stevekm about 4 years ago - 2 comments

#853 - ClusterSV Pipeline Adoption

Issue - State: closed - Opened by gongyixiao over 4 years ago
Labels: task

#852 - PCAWG_SV Merge Pipeline Adoption

Issue - State: closed - Opened by gongyixiao over 4 years ago - 3 comments
Labels: task

#851 - BRASS Pipeline Adoption

Issue - State: closed - Opened by gongyixiao over 4 years ago - 5 comments
Labels: task

#850 - PCAWG_SV Delly Pipeline Adoption

Issue - State: closed - Opened by gongyixiao over 4 years ago - 12 comments
Labels: task

#849 - SvABA Pipeline Adoption

Issue - State: closed - Opened by gongyixiao over 4 years ago - 8 comments
Labels: task

#848 - Overview of Project PCAWG_SV

Issue - State: closed - Opened by gongyixiao over 4 years ago - 9 comments
Labels: task

#776 - Some OncoKB variants are missing in the TEMPO filtered maf

Issue - State: open - Opened by ShwetaCh almost 5 years ago - 6 comments
Labels: bug, backburner

#691 - Feature/Annotate SVs

Pull Request - State: closed - Opened by kpjonsson about 5 years ago - 3 comments
Labels: enhancement

#668 - Travis-CI test for all processes

Issue - State: closed - Opened by gongyixiao over 5 years ago - 1 comment
Labels: enhancement, backburner

#612 - Trim MAF columns

Issue - State: open - Opened by kpjonsson over 5 years ago - 2 comments
Labels: enhancement, backburner

#586 - Move conpair/QcPileup related ref files into reference folder

Issue - State: open - Opened by gongyixiao over 5 years ago - 2 comments
Labels: enhancement, backburner

#568 - Sanity check exome outputs versus Roslin Megatron

Issue - State: closed - Opened by kpjonsson over 5 years ago
Labels: help wanted, question, backburner

#480 - Skip germline Manta if also running somatic?

Issue - State: closed - Opened by kpjonsson over 5 years ago - 5 comments
Labels: enhancement, backburner

#412 - Version OncoKB annotation

Issue - State: closed - Opened by kpjonsson over 5 years ago - 8 comments
Labels: enhancement, backburner

#100 - Manual Filter scripts for processing RAW MAF file

Issue - State: closed - Opened by evanbiederstedt almost 6 years ago - 6 comments
Labels: enhancement