stevekm/reportIT

Issues

• report for covid19 data

  #38 opened 2 years ago by gadepallivs
  1

• Samples with no variants not appearing in final report

  #37 opened 7 years ago by stevekm
  0

• Need to download other files from server

  #36 opened 8 years ago by stevekm
  0

• Wrong NC control sample being used for IGV snapshots

  #18 opened 8 years ago by stevekm
  0

• Change overview report sample table caption

  #35 opened 8 years ago by stevekm
  0

• GitHub info not being printed in the overview report

  #34 opened 8 years ago by stevekm
  0

• Overview report variant table and IGV snapshots are not in sync

  #33 opened 8 years ago by stevekm
  0

• need directory setup script

  #20 opened 8 years ago by stevekm
  2

• SQL integration in pipeline

  #17 opened 8 years ago by stevekm
  1

• 'find' assertions and functions

  #15 opened 8 years ago by stevekm
  1

• Need new 'sparse report'

  #5 opened 8 years ago by stevekm
  2

• run_samplesheet with qsub script does not wait for annotations to finish

  #27 opened 8 years ago by stevekm
  2

• sometimes the IGV reporting script gets hung up

  #22 opened 8 years ago by stevekm
  2

• some variants are getting left out of IGV snapshots

  #28 opened 8 years ago by stevekm
  1

• IGV_snapshot_parser.sh not passing open X server value correctly

  #32 opened 8 years ago by stevekm
  0

• paired log dir creation causes recursive symlinks

  #21 opened 8 years ago by stevekm
  2

• Variant Summary table needs to be reordered

  #31 opened 8 years ago by stevekm
  0

• bin setup script does not unzip IGV correctly

  #30 opened 8 years ago by stevekm
  1

• Need example output

  #29 opened 8 years ago by stevekm
  1

• missing deletion mutations from pipeline output

  #25 opened 8 years ago by stevekm
  1

• include snapshot zip with email

  #24 opened 8 years ago by stevekm
  0

• need script to run pipeline from samplesheet

  #26 opened 8 years ago by stevekm
  0

• IGV batchscripts need to be concatenated

  #2 opened 8 years ago by stevekm
  1

• Need to account for IonTorrent sequencing artifacts; multiple variants at locus

  #13 opened 8 years ago by stevekm
  1

• Develop database of all found variants

  #14 opened 8 years ago by stevekm
  1

• split_df_col2cols function errors on too few columns

  #1 opened 8 years ago by stevekm
  2

• Save stdout and stderr logs from active session script usage

  #23 opened 8 years ago by stevekm
  0

• Need stdout logging for interactive scripts

  #19 opened 8 years ago by stevekm
  0

• IGV snapshot dirs are making recursive symlinks

  #11 opened 8 years ago by stevekm
  1

• Report script is making reports for samples with no variants

  #12 opened 8 years ago by stevekm
  1

• Need full analysis report

  #16 opened 8 years ago by stevekm
  1

• Need pandoc bin download & setup info

  #8 opened 8 years ago by stevekm
  1

• WC IPM knowledge base integration

  #3 opened 8 years ago by stevekm
  1

• (Xvfb) IGV snapshot script does not work in parrallel

  #10 opened 8 years ago by stevekm
  1

• IGV screenshot review feedback integration

  #6 opened 8 years ago by stevekm
  3

• Need to integrate tumor & tissue type

  #9 opened 8 years ago by stevekm
  1

• WC PMKB Excel sheet variant parsing needed

  #7 opened 8 years ago by stevekm
  1

• Create wiki entries

  #4 opened 8 years ago by stevekm
  0