uclahs-cds/package-PipeVal

Issues

• Python version in README.md does not match setup.cfg

  #94 opened 6 months ago by j2salmingo
  0

• FASTQ quickcheck

  #92 opened 7 months ago by yashpatel6
  0

• Add formatter for style consistency

  #91 opened 7 months ago by yashpatel6
  0

• Path argument validation in argparse

  #90 opened 7 months ago by yashpatel6
  0

• Add locking for validation printing

  #87 opened 7 months ago by yashpatel6
  1

• Additional checksum type support

  #82 opened a year ago by yashpatel6
  0

• `gzip` file validation with `gzip -t`

  #53 opened a year ago by yashpatel6
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• `python-magic` for file type detection and checks

  #73 opened a year ago by yashpatel6
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• VCF quickcheck

  #76 opened a year ago by yashpatel6
  1

• Replace `Path` in unit tests with mocks

  #49 opened a year ago by aholmes
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• Implement unit tests for generate_md5 and generate_sha512

  #32 opened a year ago by aybeshlikyan
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• Add function to get chromosome naming convention

  #71 opened a year ago by madisonjordan
  1

• Link to "initial design" in readme is not accessible.

  #38 opened a year ago by aholmes
  0

• Update PR template

  #68 opened a year ago by madisonjordan
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• Install additional dependencies, e.g. samtools

  #39 opened 2 years ago by aholmes
  0

• Missing checksum module in Dockerfile

  #65 opened a year ago by yashpatel6
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• Check BAM index

  #50 opened 2 years ago by tyamaguchi-ucla
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• Ubuntu 20.04 update Dockerfile fix

  #61 opened 2 years ago by yashpatel6
  2

• Instructions for adding/updating as submodule

  #59 opened 2 years ago by madisonjordan
  3

• Add repo source label

  #55 opened 2 years ago by aybeshlikyan
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• Add auto-build workflow

  #54 opened 2 years ago by aybeshlikyan
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• Set default for `validate -t`

  #51 opened 2 years ago by tyamaguchi-ucla
  0

• Empty BAM check

  #47 opened 2 years ago by yashpatel6
  1

• Release 3.0.0(-rc.1)?

  #43 opened 2 years ago by tyamaguchi-ucla
  2

• Add graceful handling for the rest of the file types

  #41 opened 2 years ago by aybeshlikyan
  0

• Update documentation regarding -o argument

  #19 opened 2 years ago by aholmes
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• Add CI/CD base yaml

  #21 opened 2 years ago by tyamaguchi-ucla
  1

• Test handling of no-extension files

  #31 opened 2 years ago by aybeshlikyan
  0

• Validation error hangs nextflow pipeline instead of erroring out

  #17 opened 2 years ago by ginakkiim
  5

• Restructure code to incorporate dynamic dispatching (for specific file validation)

  #6 opened 4 years ago by ginakkiim
  0

• Clean up exception handling for file type detection

  #14 opened 3 years ago by ginakkiim
  0

• `sha512-gen` command doesn't generate sha512

  #28 opened 2 years ago by tyamaguchi-ucla
  3

• Files containing multiple "." can cause "File type does not match extension" error

  #25 opened 3 years ago by rhughwhite
  5

• file-fastq causes validation script to fail

  #26 opened 3 years ago by jmlivingstone
  1

• Add GNU open source license doc to repo

  #22 opened 3 years ago by ginakkiim
  0

• Come up with a better name for the validation tool

  #23 opened 3 years ago by ginakkiim
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• Handle paired files (on the nextflow side)

  #7 opened 4 years ago by ginakkiim
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• Adding hash verification

  #13 opened 3 years ago by ginakkiim
  0

• blcdsdockerregistry/validate:2.0.0 has many high vulnerabilities

  #9 opened 3 years ago by tyamaguchi-ucla
  1

• No validate done with -t is not set

  #18 opened 3 years ago by jmlivingstone
  0

• Error: df.fastq.gz argument of type 'NoneType' is not iterable

  #15 opened 3 years ago by ginakkiim
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• Handling generic file types that aren't explicitly stated

  #16 opened 3 years ago by ginakkiim
  1

• validate file-fasta failed on *.fa

  #8 opened 3 years ago by zhuchcn
  0

• blcdsdockerregistry/validate:2.0.0 docker image may not contain required modules?

  #10 opened 3 years ago by tyamaguchi-ucla
  0