mskcc/tempo

Issues

• storeDir option doesn't work for all modules

  #1000 opened 10 days ago by anoronh4
  1

• Facets output incompatible with Facets Preview

  #988 opened 2 months ago by anoronh4
  1

• conpair channel bug

  #1014 opened 4 months ago by anoronh4
  0

• use Channel.interval() factory instead of watchPath

  #1009 opened 7 months ago by anoronh4
  1

• replace or upgrade delly

  #1011 opened 6 months ago by anoronh4
  0

• Add assay type to MultiQC output.

  #1010 opened 7 months ago by price0416
  0

• Original quality scores are not kept in bams after BQSR

  #947 opened 8 months ago by anoronh4
  1

• clean up ngi-genomes folder

  #1007 opened 9 months ago by anoronh4
  0

• Broken links in documentation

  #998 opened 9 months ago by johnoooh
  0

• remove pipeline.nf from docs for dsl2

  #1004 opened 9 months ago by anoronh4
  0

• Aggregate from Path will fail in certain aggregation process when certain samples have non-complete subworkflow

  #1002 opened 10 months ago by gongyixiao
  0

• update multiqc

  #999 opened a year ago by anoronh4
  0

• Improvement for cohort multiqc report html

  #997 opened a year ago by gongyixiao
  0

• brass fails when input bai file does not having the expected naming convention

  #994 opened a year ago by anoronh4
  0

• update pipeline DAG visualization in documentation

  #992 opened a year ago by anoronh4
  0

• lohhla read.table bug

  #989 opened a year ago by anoronh4
  0

• Bug with biocircos plotting

  #984 opened a year ago by anoronh4
  0

• nextflow updates causing errors in execution

  #978 opened 2 years ago by anoronh4
  3

• Remove unnecessary files from SvABA published files

  #982 opened 2 years ago by anoronh4
  2

• revise normal depth cutoff for variants

  #915 opened 3 years ago by anoronh4
  1

• error in `GermlineCombineChannel`

  #903 opened 3 years ago by anoronh4
  3

• facets-suite-preview Docker base image origin undocumented.

  #939 opened 2 years ago by gongyixiao
  1

• Maf files from GenomeNexus

  #928 opened 3 years ago by price0416
  1

• Mutect2 column is enforced in germline calls even though mutect is not used

  #916 opened 3 years ago by anoronh4
  1

• Rescue mutations that are oncogenic at 2% frequency

  #922 opened 3 years ago by anoronh4
  1

• Update oncoKB annotator version

  #936 opened 3 years ago by gongyixiao
  1

• Singularity runOptions add parameters to avoid loading home directory libraries for R or Python

  #938 opened 3 years ago by gongyixiao
  0

• minor issues in logic for dsl2

  #975 opened 2 years ago by anoronh4
  0

• Zygosity annotation of mutations should be done with hisens rather than purity

  #967 opened 2 years ago by anoronh4
  1

• Optimize this line using wild card to shorten the printed command.

  #964 opened 2 years ago by gongyixiao
  0

• sampleQC_wf:SampleRunMultiQC won't run for WGS because no CollectHsMetrics is run.

  #974 opened 2 years ago by gongyixiao
  0

• SomaticCombineMutect2Vcf force sample name override header

  #976 opened 2 years ago by gongyixiao
  0

• calculate cdna contamination

  #926 opened 2 years ago by anoronh4
  0

• ClusterSV and SVSignature need to handle empty input bedpe

  #977 opened 2 years ago by gongyixiao
  0

• SampleRunMultiQC not running for WGS mode

  #957 opened 3 years ago by gongyixiao
  1

• MergeBamsAndMarkDuplicates resource allocation wrong.

  #952 opened 3 years ago by gongyixiao
  0

• QcAlfred bug

  #953 opened 3 years ago by anoronh4
  0

• Filtering BRCA Exchange Variants not working properly

  #932 opened 3 years ago by gongyixiao
  0

• Conpair completes successfully, but has empty output

  #940 opened 3 years ago by anoronh4
  1

• Error in `SampleRunMultiQC` and `CohortRunMultiQC`

  #920 opened 3 years ago by anoronh4
  0

• Make QC summary available for other trackers to use.

  #921 opened 3 years ago by anoronh4
  2

• supporting svtools

  #912 opened 3 years ago by anoronh4
  1

• `QcConpair` exits with error

  #924 opened 3 years ago by anoronh4
  1

• add_tag function bug for filter-*-maf.R

  #918 opened 3 years ago by anoronh4
  0

• switch agilent v3 files to agilent v4

  #901 opened 3 years ago by anoronh4
  1

• Hard-coded genome version need to be fixed.

  #913 opened 3 years ago by gongyixiao
  0

• support ora sequencing record files

  #911 opened 3 years ago by anoronh4
  0

• fix count of normal forward and reverse read count

  #897 opened 3 years ago by anoronh4
  1

• Missing Sample Name in Cohort Level SV

  #906 opened 3 years ago by arichards2564
  1

• limit input volume from csv over time

  #898 opened 4 years ago by anoronh4
  1