eastgenomics/eggd_dias_batch

Issues

• initial unarchive check doesn't use CNV job ID for excluded intervals bed check

  #221 opened 4 months ago by jethror1
  0

• panels and single genes in same report don't have a nice separator like multiple genes

  #220 opened 4 months ago by jethror1
  0

• Single gene file naming

  #214 opened 5 months ago by rklocke
  2

• Mismatch in total samples run in summary report

  #199 opened 5 months ago by jethror1
  1

• Improve description of non-reference file placeholders in the config file design section of README

  #206 opened 5 months ago by growland2
  0

• strip leading / trailing whitespace from user string inputs

  #207 opened 5 months ago by Addy81
  0

• batch does not unarchive all files for reanalysis

  #195 opened 5 months ago by chrispyatt
  7

• Ensure all files unarchived

  #196 opened 5 months ago by jethror1
  1

• lack of test code in manifest not flagged

  #197 opened 5 months ago by chrispyatt
  1

• Subset + manifest validation

  #198 opened 5 months ago by Addy81
  1

• Unarchive tag incorrect

  #205 opened 6 months ago by chrispyatt
  2

• prettier error message

  #204 opened 6 months ago by jethror1
  0

• Readme suggests -iassay is optional

  #172 opened 10 months ago by Addy81
  1

• incorrect docstring

  #168 opened 10 months ago by jethror1
  0

• minor log clean up

  #169 opened 10 months ago by jethror1
  0

• default to excluding controls

  #170 opened 10 months ago by jethror1
  0

• add samples specified to exclude to logs

  #173 opened 10 months ago by jethror1
  0

• ResearchUse code breaks batch

  #181 opened 10 months ago by chrispyatt
  5

• pass multiqc report as an input

  #179 opened 10 months ago by kjwinfield
  0

• mosaic reports output directory doesn't include version/datetime info

  #186 opened 10 months ago by chrispyatt
  3

• Launches all reports but fails at the end and doesn't output a summary

  #189 opened 10 months ago by Addy81
  0

• write_summary_report fails when trying to record excluded file IDs

  #191 opened 10 months ago by chrispyatt
  0

• Add an option to ignore samples in manifest

  #187 opened a year ago by Emma-MacK
  3

• automate CNV indications stripping

  #178 opened a year ago by kjwinfield
  2

• Reanalysis name matching

  #85 opened a year ago by Addy81
  2

• eggd_dias_batch mosaic calling

  #163 opened a year ago by kjwinfield
  0

• outdated warning

  #165 opened a year ago by kjwinfield
  0

• Commas within panel names

  #106 opened a year ago by rklocke
  2

• When a report isn't launched the samples are not listed in the report

  #136 opened a year ago by Addy81
  2

• Reports summary gets uploaded even if reports fail to start

  #78 opened a year ago by Addy81
  1

• Check if the files gathered are archived or not

  #77 opened a year ago by Yu-jinKim
  3

• Expand on use cases and available options for this script.

  #107 opened a year ago by Addy81
  2

• switch unarchiving to API method

  #151 opened a year ago by jethror1
  1

• Improve 'single' gene panel name for reports

  #138 opened a year ago by jethror1
  1

• move patterns used for matching samplenames to config

  #124 opened a year ago by jethror1
  0

• don't raise RuntimeError on some archived files

  #116 opened a year ago by jethror1
  0

• v3.0.0 request: Make -iexclude_samples take a file as input

  #115 opened a year ago by Addy81
  1

• Update timeout policy to CNV calling

  #109 opened a year ago by Addy81
  3

• Reanalysis of only one single gene makes workflow to fail

  #104 opened 2 years ago by Addy81
  2

• incorrect dict keys in parse_Gemini_manifest

  #101 opened 2 years ago by sophie22
  0

• CNVreports cannot resolve input folder if CNV calling was ran multiple times

  #93 opened 2 years ago by sophie22
  0

• Dias fails to run after egg_conductor due to folder name

  #94 opened 2 years ago by RSWilson1
  0

• Readme update

  #84 opened 2 years ago by Addy81
  0

• Upload excluded samples tsv to output folder

  #86 opened 2 years ago by Aisha-D
  1

• Find reports with pattern "xlsx" rather than "xls"

  #87 opened 2 years ago by Aisha-D
  0

• Raise error if the manifest contains a gene symbol

  #74 opened 2 years ago by Yu-jinKim
  0

• Report job file doesn't filter out NA samples

  #72 opened 2 years ago by Yu-jinKim
  0

• Run MultiQC with a bigger instance for TWE runs.

  #67 opened 3 years ago by Addy81
  1

• QC requires /output/dias_single/dias_multi

  #45 opened 3 years ago by Yu-jinKim
  1

• Matching naming of athena and vcf2xls reports

  #54 opened 3 years ago by Addy81
  1