nf-core/viralintegration

Issues

• v1.0.0 Release Criteria

  #51 opened 2 years ago by edmundmiller
  0

• Add subworkflows

  #58 opened 2 years ago by alyssa-ab
  0

• Add MetaPhlAn 3.0 module

  #2 opened 3 years ago by allaway
  1

• STAR Failure - roll back version

  #55 opened 2 years ago by alyssa-ab
  1

• Add viRNAtrap to pipeline

  #56 opened 2 years ago by allaway
  0

• Processes to turn into a subworkflow

  #53 opened 2 years ago by edmundmiller
  0

• Documentation push

  #50 opened 2 years ago by edmundmiller
  0

• Update test data for nf-test/summary_report

  #37 opened 2 years ago by alyssa-ab
  2

• Check scripts are up-to-date before initial release

  #46 opened 2 years ago by emiller88
  0

• Update documentation and add example analysis

  #48 opened 2 years ago by lewynli
  0

• Pipeline terminated prematurely with Exception thrown in fastq_polyA_stripper.py

  #44 opened 2 years ago by lewynli
  2

• Write basic nf-tests

  #39 opened 2 years ago by edmundmiller
  0

• Look into failing md5sums on CI

  #47 opened 2 years ago by edmundmiller
  0

• Loop in results to multiqc

  #32 opened 2 years ago by edmundmiller
  2

• Remove duplicates

  #11 opened 2 years ago by edmundmiller
  0

• Add local module labels

  #35 opened 2 years ago by edmundmiller
  0

• SummaryReport

  #28 opened 2 years ago by edmundmiller
  3

• Use CTAT singularity image

  #21 opened 2 years ago by edmundmiller
  1

• ExtractEvidenceReads

  #29 opened 2 years ago by edmundmiller
  1

• Look into License

  #26 opened 2 years ago by edmundmiller
  1

• Virus Insertion Viewer

  #6 opened 2 years ago by emiller88
  1

• Virus Infection Evidence Viewer

  #7 opened 2 years ago by emiller88
  1

• Use a small human reference for test data

  #31 opened 2 years ago by emiller88
  5

• Genome plot doesn't output anything

  #27 opened 2 years ago by edmundmiller
  0

• Pass Index Files into ExtractChimericGenomicTargets

  #33 opened 2 years ago by alyssa-ab
  0

• Virus insertion site candidates and read counts

  #5 opened 2 years ago by emiller88
  1

• VirusReport

  #23 opened 2 years ago by emiller88
  0

• Add in STAR Alignment

  #4 opened 2 years ago by emiller88
  1

• Replace bamsifter with deepTools bamCoverage

  #25 opened 2 years ago by emiller88
  0

• InsertionSiteCandidates

  #10 opened 2 years ago by emiller88
  1

• Add RemoveDuplicates

  #20 opened 2 years ago by emiller88
  2

• CTAT-VIF lib integration subworkflow

  #15 opened 2 years ago by emiller88
  0

• PolyA_stripper

  #9 opened 2 years ago by emiller88
  2

• Trimmomatic

  #8 opened 3 years ago by emiller88
  3

• Create dummy fastq data for testing

  #3 opened 3 years ago by allaway
  2