NationalGenomicsInfrastructure/ngi_pipeline

Issues

• If this is a joke about how Swedes pronounce "w"

  #377 opened 7 years ago by mariogiov
  0

• Non-existant variable referenced

  #374 opened 7 years ago by b97pla
  0

• update bam2fastq.sh using latest libs

  #371 opened 7 years ago by szilvajuhos
  0

• For GATK jarfile reliant scripts, set $GATK_HOME as default

  #364 opened 8 years ago by sylvinite
  0

• Rewrite everything in Python3

  #359 opened 8 years ago by mariogiov
  1

• Hire More Americans

  #356 opened 8 years ago by mariogiov
  1

• Fastq files are not organized under the correct library prep

  #351 opened 8 years ago by b97pla
  0

• Fastq_screen and fastqc overwrites result if fastq files has same name

  #348 opened 8 years ago by parlundin
  0

• Duplication metrics parsing ignores multiple library preps

  #340 opened 9 years ago by b97pla
  0

• No files are synced when you start the NGI pipeline with the -k flag.

  #318 opened 9 years ago by Smeds
  0

• Running NGI pipeline with multiple flowcells

  #312 opened 9 years ago by Smeds
  1

• Changing delivery status when reanalysing sample

  #309 opened 9 years ago by parlundin
  0

• Specific versions in the requirements cause conflicts

  #306 opened 9 years ago by b97pla
  1

• flowcells in a2015179 not found

  #301 opened 9 years ago by b97pla
  3

• Analysis files from wrong samples removed

  #298 opened 10 years ago by parlundin
  5

• AttributeError: 'exceptions.KeyError' object has no attribute 'msg'

  #294 opened 10 years ago by b97pla
  3

• Analysis deletion should reset Charon status values

  #292 opened 10 years ago by mariogiov
  1

• helper script: determine what step Piper is working on

  #194 opened 10 years ago by mariogiov
  3

• Decide how to track genotyping in the piper_ngi code

  #274 opened 10 years ago by mariogiov
  5

• Move CharonSession code to the charon repo

  #280 opened 10 years ago by b97pla
  0

• Track qc jobs in local jobs database

  #275 opened 10 years ago by mariogiov
  0

• restrict_to_projects by project id or project name

  #216 opened 10 years ago by mariogiov
  1

• Make it possible to pass either the project name, project id, or path when starting analysis from the project level

  #217 opened 10 years ago by mariogiov
  1

• When restarting a Piper analysis job, we should remove the old coverage value

  #252 opened 10 years ago by mariogiov
  3

• symbolic link proj_name->proj_id not created under DATA or ANALYSIS

  #233 opened 10 years ago by mariogiov
  1

• ngi_pipeline_start qc (flowcell/project)

  #253 opened 10 years ago by mariogiov
  0

• Don't start qc pipeline if it's already _running_

  #260 opened 10 years ago by mariogiov
  0

• Don't redo qc analysis if it's already done

  #254 opened 10 years ago by mariogiov
  1

• CharonSession() can time out I think

  #207 opened 10 years ago by mariogiov
  7

• If a seqrun or libprep is manually set to FAILED and bam files are present, they still are copied to scratch

  #224 opened 10 years ago by mariogiov
  1

• Delete files when re-running instead of rotating to previous_analyses

  #214 opened 10 years ago by mariogiov
  3

• Is the pipeline copying Pipers hidden files?

  #203 opened 10 years ago by johandahlberg
  7

• Fix so we can process multiple flowcells simultaneously

  #200 opened 10 years ago by mariogiov
  2

• NGI Node information in XML setup file

  #243 opened 10 years ago by ewels
  6

• Piper sbatch script should check for the exit status of the rsync process before writing PIPER_EXIT_CODE to the .out file

  #220 opened 10 years ago by mariogiov
  1

• If we can't define a libprep for a seqrun, a sample object with no libpreps will exist

  #222 opened 10 years ago by mariogiov
  0

• add "exclude_sample" and "exclude_project" to helper scripts

  #219 opened 10 years ago by mariogiov
  0

• Fix sample sheet parser to work with new sample sheets

  #204 opened 10 years ago by mariogiov
  4

• Copy version report when we rotate files

  #213 opened 10 years ago by mariogiov
  0

• Update the project regex pattern for Uppsala

  #205 opened 10 years ago by Smeds
  0

• Xten run failed, wrong name of sample folders

  #198 opened 10 years ago by Galithil
  5

• Copy logs back from scratch even if Piper run fails

  #190 opened 10 years ago by mariogiov
  1

• When rotating files from previous analyses, copy only the relevant sample

  #191 opened 10 years ago by mariogiov
  1

• I broke it

  #193 opened 10 years ago by mariogiov
  1

• Don't copy files back from scratch if piper fails

  #179 opened 10 years ago by mariogiov
  4

• ngi_pipeline_start.py will fail if not --restart-all-jobs is specified

  #186 opened 10 years ago by guillermo-carrasco
  2

• Add group sticky bit to directories created by the pipeline

  #184 opened 10 years ago by mariogiov
  6

• seqrun-level: DATA_FAILED vs. COMPUTATION_FAILED

  #178 opened 10 years ago by mariogiov
  3

• Autosomal coverage in Charon

  #173 opened 10 years ago by parlundin
  6

• Cron job to update Charon and send relevant emails

  #171 opened 10 years ago by mariogiov
  2