uab-cgds-worthey/quac

Issues

• Supplying list of files for external FASTQC causes pipeline to fail

  #95 opened 6 months ago by wilkb777
  0

• Please add documentation on how to set QC limits

  #85 opened a year ago by Redmar-van-den-Berg
  1

• Feature request: add support for specifying samples directly

  #86 opened a year ago by Redmar-van-den-Berg
  2

• System testing CI workflow gets triggered twice and one of them (tends to) fail

  #79 opened 2 years ago by ManavalanG
  7

• Have users try out QuaC in Slurm cluster which is not cheaha.

  #77 opened a year ago by ManavalanG
  0

• CLI script not accounting for user's environment specific slurm args requirements

  #76 opened a year ago by ManavalanG
  1

• Github actions for system testing failed with error "No space left on device"

  #78 opened 2 years ago by ManavalanG
  1

• Make system testing github actions run faster

  #74 opened 2 years ago by ManavalanG
  3

• --conda-create-envs-only results in errors - CreateCondaEnvironmentException and container creation failed

  #68 opened 2 years ago by ManavalanG
  6

• Verify singularity mount paths exist

  #71 opened 2 years ago by ManavalanG
  0

• Removing use of conda env for tasks within snakemake pipeline

  #69 opened 2 years ago by ManavalanG
  6

• Create a script to retrieve necessary datasets for workflow configs

  #65 opened 2 years ago by ManavalanG
  0

• document environment variables

  #66 opened 2 years ago by brentp
  3

• Set readthedocs to use master branch

  #62 opened 2 years ago by ManavalanG
  0

• Make snakemake's slurm job submission optional

  #57 opened 2 years ago by ManavalanG
  4

• Allow usage of custom slurm partitions

  #58 opened 2 years ago by ManavalanG
  0

• Update quac-watch config's median insert size threshold for WGS

  #54 opened 2 years ago by ManavalanG
  0

• Remove default configs for --quac_watch_config option

  #39 opened 2 years ago by ManavalanG
  0

• Rename default branch `master` to `main`

  #60 opened 2 years ago by ManavalanG
  0

• Identify the human sample that causes cross-sample contamination

  #46 opened 2 years ago by ManavalanG
  2

• Samples with high GC content

  #43 opened 2 years ago by ManavalanG
  5

• Need to refactor fastq_screen testing in QuaC Watch?

  #41 opened 3 years ago by ManavalanG
  1

• Why does "Per Base Sequence Content" always fail in fastqc-trimmed?

  #29 opened 2 years ago by ManavalanG
  1

• Refine QC checkup thresholds used with exome samples

  #26 opened 2 years ago by ManavalanG
  5

• Make somalier and verifybamID resource files available in datasets_central_manager

  #25 opened 2 years ago by ManavalanG
  3

• Remove prerun QC as requirement to QuaC.

  #45 opened 2 years ago by ManavalanG
  2

• Explicitly define conda environments

  #49 opened 2 years ago by ManavalanG
  4

• Use container solution for covviz installation instead of conda

  #52 opened 2 years ago by ManavalanG
  3

• Remove git submodules

  #53 opened 2 years ago by ManavalanG
  2

• Use snakemake-minimal in conda env to reduce bloat

  #56 opened 2 years ago by ManavalanG
  3

• Add somalier's "middling allele balance" metric to QuaC Watch

  #40 opened 3 years ago by ManavalanG
  0

• Check if QuaC run would create any conflict when run with small_variant_caller_pipeline

  #38 opened 2 years ago by ManavalanG
  4

• QuaC fails when only one sample in input ped file

  #34 opened 2 years ago by ManavalanG
  7

• Separate output directory option for per-sample QC results and Project-level QC results

  #55 opened 3 years ago by ManavalanG
  1

• QuaC does not support projects with mixed WGS and WES samples

  #36 opened 4 years ago by ManavalanG
  2

• Choose and add license

  #51 opened 3 years ago by ManavalanG
  0

• Is smaller median insert size a bad thing for downstream data analyses?

  #44 opened 2 years ago by ManavalanG
  2

• Number of decimal digits to show in multiqc report

  #50 opened 3 years ago by ManavalanG
  0

• QuaC stalls at singularity+conda env creation step for multiqc

  #47 opened 2 years ago by ManavalanG
  17

• Qualimap fails due to out of memory

  #48 opened 2 years ago by ManavalanG
  2

• Multiqc rules at single-sample mode wants to run everytime new samples are added to project

  #42 opened 3 years ago by ManavalanG
  5

• Potential bottenecks when moving QC from small var caller pipeline to QuaC

  #30 opened 2 years ago by ManavalanG
  1

• Create system testing to use only sample in pedigree as input

  #35 opened 2 years ago by ManavalanG
  1

• Picard CollectMultipleMetrics takes too long to run

  #37 opened 3 years ago by ManavalanG
  0

• Don't carry over host's env variables to singularity container

  #28 opened 2 years ago by ManavalanG
  2

• Would be nice to have a name for "CGDS QC checkup" tool

  #24 opened 2 years ago by ManavalanG
  5

• Multiqc-config files will run into conflict when multiple instances of QuaC is run

  #27 opened 2 years ago by ManavalanG
  6

• Automate relatedness verification based on info in input pedigree file

  #33 opened 4 years ago by ManavalanG
  0

• Automate verification of sex based on info in input pedigree file

  #32 opened 4 years ago by ManavalanG
  0

• Refactor how QuaC-Watch analyzes the results of fastqc's "Per Base Sequence Content" module results

  #31 opened 4 years ago by ManavalanG
  0